Objective To compare the regulatory effects and underlying physiological mechanisms of Pseudomonas huaxiensis M11 and Bacillus megaterium M28 on the photosynthetic characteristics of maize subjected to low soil fertility stress. Methods A pot experiment was implemented with four treatments: normal soil control (CK), low nutrient treatment (LNT), and bacterial inoculation under LNT conditions (M11+LNT, M28+LNT). At the tasseling stage, measurements were taken for soil nutrients, plant growth indices, gas exchange parameters, chlorophyll fluorescence characteristics, and the fast chlorophyll a fluorescence induction kinetics (O-J-I-P chlorophyll a fluorescence transient, OJIP curve). Yield components were assessed at physiological maturity. Results Inoculation with M11 significantly increased the content of available phosphorus, available potassium, and organic matter, while reducing the electrical conductivity in soil. M28 significantly enhanced the total nitrogen content. Both bacterial treatments significantly promoted maize growth, increasing the plant height, leaf area, SPAD value, and biomass. Moreover, they highly significantly enhanced the net photosynthetic rate (P_n), stomatal conductance (G_s), transpiration rate (T_r), and water use efficiency (WUE), while reducing the intercellular CO₂ concentration (C_i). Chlorophyll fluorescence analysis revealed a decrease in minimal fluorescence (F_o) and increases in the maximum photochemical efficiency (F_v/F_m), actual photochemical quantum yield of PSII (Φ_PSII), apparent photosynthetic electron transport rate (ETR), photochemical quenching (qP), and the fraction of open PSII centers based on excitation energy (qL), with no significant change in non-photochemical quenching (NPQ). The OJIP curves indicated the absence of a K-step in inoculated plants, a decrease in fluorescence at the J-step, and increases at the I-step and P-step. The differential kinetic curves of relative variable fluorescence (ΔV_t analysis) confirmed that both strains synchronized the optimization of electron transport on both the donor and acceptor sides of photosystem II (PSII). The increased amplitude of the I-P phase suggested enhanced photosystem I (PSI) activity. Junction-intermediate-peak test (JIP-test) parameters demonstrated that inoculation significantly enhanced the performance index based on absorbed light energy (PI_ABS), the performance index on a cross-section basis (PI_CS), the probability that a trapped exciton moves an electron into the electron transport chain beyond Q_A (Ψ_o), the quantum yield for electron transport (φ_Eo), and the electron transport flux per reaction center (ET_o/RC). Conversely, dissipated energy flux per cross-sectional area (DI_o/RC) and quantum ratio for dissipated energy (φ_Do) decreased. Consequently, compared with the LNT group, the M11 and M28 treatments resulted in significant increases of 30.61% and 22.64% in maize fresh weight and 26.68% and 23.41% in dry weight, respectively. Conclusion P. huaxiensis M11 primarily enhances photosynthetic performance by increasing soil available phosphorus and potassium content, directly optimizing energy metabolism and stomatal movement, whereas B. megaterium M28 mainly acts by elevating soil total nitrogen content, focusing on stabilizing the structure of the photosynthetic apparatus. Together, they protect the integrity of photosynthetic apparatus and optimize the electron transport efficiency of photosystems, significantly improving the photosynthetic performance and yield of maize under low fertility stress. These findings provide a theoretical basis for the targeted application of microbial inoculants in sustainable agricultural production.