Environmental pollution by heavy metals is becoming a serious problem globally. Excess Manganese (Mn) can inhibit the photosynthetic process, which consequently results in a reduction of phytoremediation of soils polluted by heavy metals. In this study, Melia azedarach which distributed widely in south China was employed as experimental material. MnCl₂ (analytically pure) (0, 10 and 30 g) were mixed with pure water first and the mixture solution was divided into 10 equal parts to add to the pots every day, respectively. They were designated as CK, L1, L2, respectively. The toxicity of Mn on photosystems behavior in leaves of Melia azedarach was investigated using in vivo chlorophyll fluorescence transients and light absorbance at 820 nm. The results showed that the excessive Mn levels induced the significant difference of the performance index (PI_ABS). The relative variable fluorescence intensity at the K-step (W_k) and relative variable fluorescence at the J-step (V_j) in Mn-treated leaves significantly higher than that of the CK. The probability of an electron moving from Q_A^- to reduce end electron acceptors at the PSⅠ acceptor (Ψ_(Ro))and probability that a trapped exciton moved an electron into the electron transport chain beyond Q_A (Ψ_(Eo)) showed an initial increase and then decrease trend. The PSI performance (ΔI/I₀) and the coordination between PSⅡ and PSⅠ (φ_(PSI/PSⅡ)) decreased in Mn-treated leaves. Also, excessive Mn significantly decreased the net photosynthetic rate and RuBP carboxylation efficiency, but increased intercellular CO₂ concentration. The results indicated that excessive Mn impaired the performances of photosystems (PSI and PSⅡ), which caused the decrease of the net photosynthetic rate and the rate of CO₂ assimilation.