Lycopene content is one of important factor for determining watermelon fruit quality. In this study, a small-type watermelon was grown in a greenhouse with supplementary red lighting 10 h per day after pollination 10 days. The results showed that supplementary red lighting promoted the lycopene accumulation earlier in watermelon flesh than the control. qRT-PCR analysis showed that among the lycopene metabolism pathway genes, ClPSY1 (phytoene synthase) expression increased significantly. Moreover, we identified PHYTOCHROME INTERACTING FACTORS 3 (ClPIF3) and bZIP transcription factor ELONGATED HYPOCOTYL 5 (ClHY5) in watermelon flesh, and red light has opposing effects on ClHY5 and ClPIF3 expression levels. The interaction experiments showed that ClHY5, a potent ClPIF3 antagonist, regulated ClPSY1 expression by directly targeting a common promoter cis-element (G-box). Collectively, our findings unraveled that ClHY5 and ClPIF3 form a dynamic activation-suppression transcriptional module responsive to red light cues to regulate watermelon lycopene accumulation.