Direct absorption methane reactor can maintain the fermentation process of microorganism by utilizing solar absorption and scattering of media in biogas reactor to improve the slurry temperature. However, direct absorption heating alone can save the corresponding electric energy and ensure the normal fermentation process of the biogas slurry in the reactor, but there are still problems of big temperature fluctuation and low solar heat absorption efficiency. In order to improve the stability of the fermentation process, it is proposed to optimize the design of this kind of reactor by filling paraffin PCM (phase change material). In this paper, a novel transient model for simulating the photo-thermal transfer process of the reactor with PCM structure was proposed. Experimental and numerical methods were utilized to analyze the effect of PCM parameters on photo-biochemical transformation process and solar heat absorption efficiency. The results show that filling paraffin phase change material in the enclosure of direct absorption reactor can effectively improve its thermal insulation and thermal storage performance, so as to improve the rate of volatile fatty acids (VFA) and gas production by anaerobic fermentation by maximum 31.1%. The average solar heat absorption efficiency of reactor equipped with PCM is bigger than 50%. Thicknesses of 4 cm and 2 cm for side and top structure were selected, respectively.