Objective To investigate the effects and mechanisms of TAR DNA-binding protein 43 (TDP-43) on oxygen-glucose deprivation (OGD)-induced apoptosis in mouse atrial myocytes (HL-1 cells). Methods The in vitro cultured mouse atrial myocytes (HL-1 cells) were divided into: (1) control group and groups with different OGD treatment times (2, 4, 8, 16 h), and cell viability was detected by CCK-8 assay, and TDP-43 protein expression level was detected by Western blotting, which was used to determine the time point of OGD induction for the subsequent study; (2) control and OGD groups, flow cytometry was used to detect apoptosis, JC-1 staining to detect mitochondrial membrane potential, chemiluminescence to detect adenosine triphosphate (ATP) relative content, microplate method to detect malondialdehyde (MDA) content, and WST-1 method to detect superoxide dismutase (SOD) content. Mouse atrial myocytes (HL-1 cells) transfected with lentivirus were divided into: (1) negative control lentiviral intervention group (NC-shRNA), TDP-43 knockdown lentiviral intervention group (TDP-43-shRNA1, TDP-43-shRNA2, TDP-43-shRNA3), and Western blotting was used to detect the TDP-43 protein expression level, and the group with the highest lentiviral knockdown efficiency was selected as the TDP-43-shRNA for subsequent experiments; (2) NC-shRNA group, TDP-43-shRNA group, OGD+NC-shRNA group, OGD+TDP-43-shRNA group, under normoxic and OGD conditions, flow cytometry was used to detect the apoptosis rate, MitoTracker staining to detect mitochondrial morphology, JC-1 staining to detect mitochondrial membrane potential, chemiluminescence to detect the relative content of ATP, flow cytometry to detect the fluorescence intensity of reactive oxygen species (ROS), microplate to detect the content of MDA, and WST-1 to detect the content of SOD. Results CCK-8 method showed that, with the prolongation of OGD time, the viability of mouse atrial myocytes (HL-1 cells) gradually decreased; Western blotting assay showed that the expression level of TDP-43 protein gradually increased, and both of them showed a strong time-dependence. Compared with control group, mouse atrial myocytes (HL-1 cells) viability was the lowest (P<0.05) and TDP-43 protein expression was the highest (P<0.05) at 16 h of OGD, accordingly, OGD 16 h was chosen as the induction time point for subsequent experiments. Compared with control group, the apoptosis rate, the fluorescence intensity ratio of mitochondrial membrane potential and the content of MDA increased, the relative content of ATP and SOD decreased in OGD group, and the differences were all statistically significant (P<0.05). Western blotting detection showed that compared with NC-shRNA group, the TDP-43-shRNA2 group had the most obvious reduction in TDP-43 protein expression level (P<0.05) and the highest knockdown efficiency, so the TDP-43-shRNA2 group was selected for subsequent experiments. The results of flow cytometry showed that under normoxic conditions, there was no significant change in the apoptosis rate in TDP-43-shRNA group compared with NC-shRNA group (P>0.05); and under OGD conditions, the apoptosis rate in OGD+TDP-43-shRNA group reduced when compared with OGD+NC-shRNA group (P<0.05). MitoTracker staining results showed that the mitochondrial morphology of TDP-43-shRNA group was intact without significant changes compared with NC-shRNA group; the mitochondria of OGD+NC-shRNA group increased in number, most of which were fragmented and scattered in distribution; compared with OGD+NC-shRNA group, the mitochondrial morphology of OGD+TDP-43-shRNA group was restored. Under normoxic conditions, there were no significant changes in mitochondrial membrane potential, relative ATP content, ROS fluorescence intensity, MDA content, and SOD content in TDP-43-shRNA group compared with NC-shRNA group (P>0.05); however, under OGD conditions, the ratio of fluorescence intensity of mitochondrial membrane potential of cells the fluorescence intensity of ROS, and the content of MDA decreased, and the relative content of ATP and the content of SOD increased in OGD+TDP-43-shRNA group compared with that of OGD+NC-shRNA group, and all of these differences was statistically significant (P<0.05). Conclusion TDP-43 exacerbates OGD-induced mitochondrial dysfunction by regulating cardiomyocyte apoptosis; therefore, knockdown of TDP-43 expression is expected to be a potential therapeutic strategy for ischemic cardiomyopathy.