Chemcial fertilizer as the main strategy for improving the vegetable yields was excessively applied in recent years which led to progressively serious soil problems such as the soil acidification. According the situation, five different biofertilizer treatments [no fertilizer (CK), inoculations of Bacillus subtilis (Bs, T1), combination of Bs and Bacillus mucilaginosus (Bs+Bm, T2), Bs and Bacillus amyloliquefaciens (Bs+Ba, T3), and Bm+Ba (T4)] were conducted to investigate the effect of the growth, leaf physiological indices, and chlorophyll fluorescence of spinach seedlings in the growth chamber. The growth and physiological indices of the spinach seedlings attained a maximum under the T2 treatments. Under the T2 treatment, the ABS/RC (Absorption flux per RC), TR0/RC (Trapping flux per RC), and ET0/RC (Electron transport flux per RC) was significantly increased, while the DI0/RC [Dissipated energy flux per RC (at t = 0)] was decreased. The OJIP curve was improved under of the inoculations of fertilizers, and the increasing range was the largest under the T2 treatment. The leaf light response curve (LC) was also significantly increased under the T2 treatment. The plant growth characteristics [leaf length (LL), leaf weight (LW), plant height (PH)] were positively correlated with the J-I-P test chlorophyll fluorescence parameters [PIABS (Performance index for energy conservation from exciton to the reduction of intersystem electron acceptors), phi P0 (Maximum quantum yield of primary photochemistry), phi E0 (Quantum yield of electron transport), psi 0 (The probability that a trapped exciton moved an electron in electron transport chain further than QA-), TR0/RC, and ET0/RC] while negatively correlated with phi D0 (Quantum yield of energy dissipation) and DI0/RC. The leaf physiological characteristics [SP (soluble protein concentrations), SC (soluble carbohydrate concentrations), Chl a (chlorophyll a), Chl b (chlorophyll b), Chl a+b, Chl a/b, and WP (water potential)] were positively correlated with the J-I-P test chlorophyll fluorescence parameters (PIABS, phi P0, phi E0, psi 0, ABS/RC, TR0/RC, and ET0/RC) while negatively correlated with phi D0 and DI0/RC. These results indicated that the combination of Bs+Bm inoculations promoted the growth of the spinach and improved the adaptability of the vegetable to acid soil while Ba inoculation didn't have any effects to plants.