Lakes constitute a significant source of atmospheric CH4, yet estimates of their emissions remain highly uncertain, partly due to an incomplete understanding of CH4’s biological sources. The phenomenon of CH4 supersaturation in surface waters, often termed the “methane paradox,” challenges the traditional view that biological CH4 production occurs only under strictly anaerobic conditions, indicating that oxic CH4 production may be possible. To investigate the cause of this surface CH4 supersaturation, this study focused on the eutrophic Gaoyang Lake. Combining field observations with incubation experiments, we examined the spatiotemporal distribution patterns of CH4 in the water column and their driving mechanisms. Field monitoring revealed a pronounced “methane paradox” in summer. CH4 in the surface water was not only supersaturated relative to the atmosphere (approximately 496 times atmospheric concentration) but was also 58% higher than in the bottom water. Incubation experiments indicated that methylphosphonate (MPn) degradation is an important source of lacustrine CH4: (1) The addition of MPn stimulated CH4 production, increasing the CH4 production rate by 68.6% compared to the control; (2) The MPn degradation process was regulated by inorganic phosphorus (Pi), as Pi addition inhibited both MPn degradation and CH4 production; (3) The addition of Pi to aerobic lake water suppressed CH4 production, reducing yield by 28% compared to the control. Furthermore, a significant negative correlation was observed between surface CH4 and soluble reactive phosphorus (SRP) (r = -0.87, p < 0.05), suggesting that decreased SRP promotes the accumulation of CH4 in surface waters. This finding further supports the inference that microbial MPn metabolism drives surface CH4 supersaturation. In summer, substantial depletion of SRP in the surface layer, coupled with thermal stratification hindering vertical nutrient transport, creates favorable conditions for MPn-based CH4 production. This study reveals the impact of phosphonate metabolism on the CH4 cycle in eutrophic lakes, providing new evidence and a theoretical perspective for understanding lake CH4 sources. These findings are significant for refining global lake greenhouse gas emission models and predicting ecosystem responses under climate change.