Objective To investigate the effect of Mex3c gene knockout on embryonic neural tube development and its possible mechanisms. Methods The NCBI database was used to analyze the expression of Mex3c gene in various tissues of mice. Fluorescence in situ hybridization (FISH) was employed to detect the expression of Mex3c in neural tubes of Mex3c^+/+ mice at different developmental stages (E12.5 d, E14.5 d). Sexual mature mice were mated at a ratio of Mex3c^+/- male to female (1:1) in the same cage. Embryos were collected and genotyped using PCR. They were divided into 3 groups based on their genotype: wild-type group (Mex3c^+/+, WT group), homozygous knockout group (Mex3c^-/-, KO group), and heterozygous knockout group (Mex3c^+/-). HE staining was employed to observe the development of neural tubes in the 3 groups of embryos. Immunofluorescence staining and Western blotting were performed to detect the proliferation and apoptosis of embryonic neural stem cells in the WT and KO groups. Transmission electron microscopy was used to observe the ultrastructure of the neural tubes and mitochondria in the WT and KO groups. RNA was extracted from the neural tubes of WT and KO groups for RNA-seq sequencing. The R.3.6.3 software was used to perform KEGG signaling pathway enrichment analysis on differentially expressed genes. RT-qPCR was used to validate the sequencing results. Results The NCBI database analysis and FISH detection results showed that the Mex3c gene was mainly expressed in the central nervous system of embryos. HE staining results showed that there was no significant difference in the development of embryonic neural tubes between KO group, WT group, and heterozygous knockout group at E12.5 d and E13.5 d. However, at E14.5 d, the embryonic neural tube development in KO group was delayed and the phenotype was significantly abnormal compared with those in WT group. Therefore, the embryonic neural tube tissues of KO group and WT group at E14.5 d were selected for subsequent experiments. The immunofluorescence staining results showed that the PCNA positive cell rate in KO group was significantly lower than that in WT group (P<0.001). The Western blotting results showed that the Bax/Bcl-2 ratio in KO group was higher than that in WT group (P<0.01). Transmission electron microscopy observation showed that compared with WT group, the synaptic gap in KO group disappeared, the mitochondrial of the embryonic neural tube in KO group were swollen, the mitochondrial cristae were disrupted, and the structure was significantly abnormal. The results of RNA-seq analysis showed that a total of 377 differentially expressed genes were obtained, including 101 up-regulated genes and 276 down-regulated genes. KEGG signaling pathway enrichment analysis revealed that the main signaling pathways of differentially expressed genes were enriched in the neuroactive ligand receptor interaction signaling pathways. The RT-qPCR validation results showed that the mRNA expression levels of Avpr1a, Drd1, Htr7, Sstr1, Oxtr and Gabra5 in this signaling pathway were down-regulated (P<0.05 or P<0.01), which was consistent with the RNA-seq results. Conclusion Mex3c plays an important role in the development of neural tubes in mouse embryos, which may participate in regulating the proliferation and apoptosis of neural stem cells through neural active ligand receptor interaction signaling pathways, thereby affecting the development of neural tubes.