Methanogenesis and methanotrophy are the processes determining methane emission from freshwater systems. The main methane consumer is methane oxidizing bacteria (MOB). MOB is known to be consumed by zooplankton as an alternative food source during winter. Seasonal MOB consumption by zooplankton based on researches of temperate lakes is well described. However, how MOB contribution to pelagic foodweb varies annually remains a pending question. To verify both the seasonal and annual pattern of MOB contribution, we monthly surveyed at a subtropic reservoir (Feitsui Reservoir, Taiwan) for four years. At the seasonal scale, MixSIR analysis including phytoplankton and methanotroph as the two food sources revealed that MOB contribution rose in winter (maximal 14.6%) and was the lowest during summer. At the annual scale, we proposed two non-contradictory hypotheses that (i) profundal hypoxia in summer and/or (ii) oxygen supply to bottom in winter enhances MOB production and contribution to zooplankton diet. We constructed a one-dimensional model to clarify the hydrological mechanism, accounting for annual variations in MOB contribution to pelagic foodweb. Our field data and simulation results support the first hypothesis that summer profundal hypoxia increases MOB consumption by pelagic consumers in winter.