This study investigated the synergistic effects and regulation strategy of multiple factors for improving methane production in sequencing batch dry anaerobic digestion (SBD-AD) using corn stalks (CS) and cow dung (CD). The regulation of the spray frequency (SF) and inoculum content (IC) significantly improved methane yield, which increased feedstock ratios (FRs) by 12.4-121.3%. Moreover, the relationship between SF and IC produced distinct interaction modes. An FR of 4:6 increased the SF to 2 h for the CD-rich condition, and an FR of 6:4 decreased the SF during a 6 h interval and increased the IC for the CS-rich condition, resulting in increases in methane yield and the conversion efficiency of volatile fatty acids (VFAs). Methanogenesis (Methanogens) played a key role in SBD-AD. The nutrient substrate (NH4-N+) and key enzyme activities of methanogens were significantly affected such that the synergistic effect of the acetoclastic and hydrogenotrophic methanogenesis pathways was likely strengthened.