Methane oxidation affects hydrocarbon accumulation and carbon cycling with important geological and paleoclimatic responses. However, the petrological and geochemical evidences that can clearly discern anaerobic (AOM) and thermochemical (TOM) oxidations in petroliferous basins are unclear, causing the disputes if these two processes can take place in specific conditions. Here, the Baikouquan Formation (T1b) in the Mahu Sag, Junggar Basin, China, was used as the first case study for comprehensive petrological and geochemical analyses to explore this scientific issue. Results indicate that the two main types of T1b calcite cement record different methane oxidation mechanisms. Calcite cements filling intergranular pores were formed during early diagenesis in relatively shallow-burial stages, through AOM with high-valence Mn oxides as electron acceptors, and with compositions of −47.5 ‰ < δ13C < −30.9 ‰, 1.1 wt% < MnO < 5.8 wt%, and 0.02 wt% < FeO < 0.13 wt%. Calcite cements filling intragranular dissolution pores were formed through TOM with high-valence Mn oxides as electron acceptors during mesogenesis during relatively deep-burial stages, with compositions of −39.7 ‰ < δ13C < −14.3 ‰, 0.43 wt% < MnO < 11.00 wt%, and 0.03 wt% < FeO < 0.36 wt%. Thus, methane oxidation underwent a transition from AOM to TOM with increasing depth, as recorded by the calcite cements with different occurrences. This transition may be a common feature of clastic strata in petroliferous basins.