Methyl jasmonate (MeJA) is involved in regulating various growth and development processes of plants, yet the underlying mechanisms remain unclear. Therefore, the objective of this study was to investigate the effects of exogenous MeJA on physiological growth, photosynthesis, and endogenous hormones in soilless cultivated Chinese chives. Four concentrations of MeJA (0, 300, 500, and 800 μM) were applied to the leaves of substrate-grown and hydroponics Chinese chives. The results showed that MeJA increased the leaf tissues water content and SPAD values of hydroponically Chinese chives, and 500 μM MeJA significantly enhanced the root activity and leaf carotenoids content of soilless cultivated Chinese chive, and promoted the activities of key enzymes of chlorophyll synthesis (ChlM and POR), thereby increasing chlorophyll a, chlorophyll b and total chlorophyll contents. Meanwhile, MeJA (500 μM) enhanced the activity of key enzymes in the Calvin cycle (Rubisco, FBA, FBPase, GAPDH, and TK), promoted CO2 fixation, improved photosynthetic carbon assimilation efficiency, and promoted Gs, Tr, and Pn, thereby enhancing photosynthesis. Moreover, MeJA (500 μM) significantly enhanced the instantaneous distribution (I-P) of the OJIP curve, enhanced the ability of the plastoquinone pool (PQ) to accept electrons, increased the quantum yield, promoted the apparent quantum flux per unit leaf area and energy flux ratio per unit PSII active reaction center, improved the electron transfer efficiency while reducing the heat dissipation energy flux per unit PSII active reaction center, and thus enhanced PSII activity. Additionally, exogenous MeJA (500 μM) promoted the accumulation of endogenous ZT, GA3, IAA, and ABA, but inhibited the upstream substrates for OPDA synthesis (MGDG and DGDG) in the JA synthesis pathway, and decreased the activities of JA synthases (LOX, AOC, and OPR), which in turn inhibited the synthesis of JA and MeJA. Changes in the relative content of MGDG/DGDG altered the membrane lipid composition of the photosynthetic membrane, which in turn altered the energy balance of the light reaction and improved the efficiency of electron transfer within the photosynthetic membrane, thereby enhancing the photosynthetic capacity. In conclusion, our study demonstrates that exogenous MeJA improves root activity and chlorophyll accumulation in soilless cultured Chinese chives, and adjusting the composition of photosynthetic membrane lipids by regulating the levels of endogenous hormones and JA-synthesizing substrates, promoting the efficiency of electron transfer, enhancing PSII activity, and promoting photosynthetic carbon fixation, thereby enhancing photosynthesis and promoting growth.