Atmospheric cold plasma (ACP) is a potential green preservation technology, but its preservation mechanism is still unclear, and the effects of different plasma intensities on postharvest tomatoes are little studied. In this study, the effects of different ACP treatments (0 kV, 40 kV, 60 kV, and 80 kV) on the sensory quality, physiological indexes, key enzyme activities, and gene expression related to the chlorophyll metabolism of postharvest tomatoes were investigated during the storage time. The results showed that compared with the control group, the tomatoes in the plasma treatment group had a higher hardness and total soluble solid (TSS) and titratable acid (TA) contents, a lower respiratory intensity and weight loss rate, a higher brightness, and a lower red transformation rate, especially in the 60 kV treatment group. In addition, chlorophyll degradation, carotenoid accumulation, and chlorophyllase and pheophorbide a mono-oxygenase (PAO) enzyme activities in the postharvest tomatoes were inhibited in the 60 kV treatment group, and the expressions of three key genes related to chlorophyll metabolism, chlorophyll (CLH1), pheophytinase (PPH), and red chlorophyll catabolic reductase (RCCR) were down-regulated. The results of the correlation analysis also confirmed that the enzyme activity and gene expression of the chlorophyll metabolism were regulated by the ACP treatment, aiming to maintain the greenness of postharvest tomatoes.