Inherent characteristics of complex organic components and their interactive coupling with environmental factors limit the comprehensive understanding of biotransformation in anaerobic digestion. In this study, we elucidated the mechanism underlying an interesting phenomenon, where a non-additive effect for methane production was recorded when primitive components, i.e., alpha-cellulose (α-CE), xylan (XY), and alkali lignin (AL), were used. The interaction of α-CE and XY produced a supra-additive effect due to the reduction of the energy barrier of carbonyl compound degradation. The degradation of non-conjugated CO, with lower kinetic stability, was preferred to the degradation of conjugated CO. The introduction of AL produced a sub-additive effect, and AL exerted a stronger inhibitory effect on the methanogenesis of XY than α-CE. The preferential change in the relevant structural units occurred due to the deposition of AL on the surface of XY or the wrapping of XY by AL. In this study, we described a multiphase integrated influence mechanism, which can be used to more effectively design anaerobic co-digestion strategies and achieve the controlled enhancement of methane yield of perishable organic solid waste.