Geological evidence indicates that the deglaciation of Marinoan snowball Earth ice age (similar to 635Myr ago) was associated with intense continental weathering, recovery of primary productivity, transient marine euxinia, and potentially extensive CH4 emission. It is proposed that the deglacial CH4 emissions may have provided positive feedbacks for ice melting and global warming. However, the origin of CH4 remains unclear. Here we report Ni isotopes (delta Ni-60) and Yttrium-rare earth element (YREE) compositions of syndepositional pyrites from the upper most Nantuo Formation (equivalent deposits of the Marinoan glaciation), South China. The Nantuo pyrite displays anti-correlations between Ni concentration and delta Ni-60, and between Ni concentration and Sm/Yb ratio, suggesting mixing between Ni in seawater and Ni from methanogens. Our study indicates active methanogenesis during the termination of Marinoan snowball Earth. This suggests that methanogenesis was fueled by methyl sulfides produced in sulfidic seawater during the deglacial recovery of marine primary productivity.