Based on the literature on the degradation mechanism and the change of micro-functional groups in the fermentation process of modified rice straw, this study aimed to solve the problems of low biogas production rate and poor stability of the biogas production system. In this work, mathematical equations were developed and combined with duck dung and rice straw mixed raw material to perform a fermentation test. The molecular micro-functional group changes of cellulose, hemicellulose, and lignin were studied to obtain the optimal ratio of mixed raw materials for fermentation and to explore the optimization mechanism of its fermentation biogas production. Experimental results showed that the optimal ratio of mixed raw materials was 2.8:1, and the inclusion of a suitable amount of Mn2+(concentration of 2 mol × L-1) was able to strengthen MnP activity and improve the ability of white-rot fungi to rupture β-O-4 bonds. A modification pre-treatment via activated carbon-based solid acid was performed, and the experimental group generated 15.8% more cumulative biogas than the control group. The biogas yield reached its peak when 300 g of inoculum was added to the pre-treatment at a concentration of 30%.