Excess and deficient nitrogen (N) inhibit photosynthesis in the leaves of rice plants, but the underlying mechanism is still unclear. N can improve the chlorophyll content and thus affect photon absorption, but the photosynthetic rate does not increase accordingly. To investigate this mechanism, three concentrations of N treatments were applied to two rice varieties, Zhefu802 and Fgl. The results indicated increased chlorophyll content of leaves with an increased N supply. Little discrepancy was detected in Rubisco enzyme activity and Non-photochemical quenching (NPQ) in the high nitrogen (HN) and moderate nitrogen (MN) treatments. The model that photoinhibition occurs in Zhefu802 due to a lack of balance of light absorption and utilization is supported by the higher malondialdehyde (MDA) content, higher H 2 O 2 content, and photoinhibitory quenching (qI) in HN treatment compared with MN treatment. A lower proportion of N in leaf was used to synthesize chlorophyll for Fgl compared with Zhefu802, reducing the likelihood of photoinhibition under HN treatment. In conclusion, HN supply does not allow ideal photosynthetic rate and increases the likelihood of photoinhibition because it does not sustain the balance of light absorption and utilization. Apart from Rubisco enzyme activity, NPQ mainly contributes to the unbalance. These results of this study will provide reference for the effective N management of rice. Int. J. Mol. Sci. 2020, 21, 2115 2 of 17 reaction center, resulting in 3P680 * , a triple state of the chlorophyll molecules [11]. The triple molecules can react with O 2 to generate deleterious singlet O 2 ( 1 O 2 ) [12], degrade the PSII reaction center protein D1, inactivate PSII and inhibit photosynthesis [13]. To eliminate damage from excessive light, plants have evolved some photoprotective mechanisms [7]. One mechanism is to dissipate the excessive excitation energy as heat in PSII antenna complex, which is known as non-photochemical quenching (NPQ) of chlorophyll fluorescence [14,15]. Although ubiquitous, the role of NPQ in plant productivity remains uncertain because it momentarily reduces the quantum efficiency of photosynthesis. Hubbart et al. [16] assessed photoprotection in rice at the whole canopy scale, and demonstrated that compared to wild-type plants, the overexpression of PsbS resulted in higher NPQ, increased canopy radiation use efficiency, and grain yield in fluctuating light. Genotypic variation of NPQ in rice was observed under natural solar radiation [17]. Wang et al. [8] reported that OsPsbS1 explains more than 40% of the NPQ variation. According to the induction speed of the relaxation kinetics curve in the dark, NPQ can be divided into three main components: qE, energy-dependent quenching, or fast NPQ, which is induced in seconds and is based on the proton gradient across the thylakoid membrane; qT, state transition quenching, or middle NPQ, which is induced in minutes; and the third component, qI, photo-inhibition quenching, or slow NPQ, which is induced very slowly [18,19]. The ...