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Chlorophyll plays essential roles in photosynthesis and its degradation should be regulated precisely. Chlorophyll b reductase encoded by the gene NYC1 is responsible for catalyzing chlorophyll b degradation and maintaining the stability of photosystems. Although NYC1s have been characterized in many plants, their function in the photosynthetic machinery and the underlying regulatory mechanisms at the whole transcriptome level remain elusive. In this study, the ZjNYC1 gene was cloned from the important warm-season turfgrass Zoysia japonica. Analysis of the subcellular localization revealed that ZjNYC1 was localized in the chloroplasts, and results of the bimolecular fluorescence complementation (BiFC) assay indicated that ZjNYC1 could interact in vivo with the NYC1-like protein, ZjNOL. Overexpression of ZjNYC1 accelerated the degradation of chlorophyll, and promoted senescence with accumulation of ABA and reactive oxygen species (ROS) in Arabidopsis. Expression of ZjNYC1 rescued the stay-green phenotype of the Arabidopsis nyc1 mutant. An integrated analysis of chlorophyll fluorescence test (JIP-test) and RNA-sequencing revealed that ZjNYC1 negatively affected the efficiency of the PSII, PSI, and the intersystem electron transport chain. Furthermore, the Calvin cycle and photorespiration were suppressed, but ABA and ethylene synthesis and signal transduction pathways were activated in the transgenic lines. Collectively, these results demonstrated that ZjNYC1 plays important roles in accelerating chlorophyll degradation and senescence, and caused negative affect on the integrity and functionality of the photosystems.