The anaerobic digestion (AD) technology has been widely used to convert biowaste to bioenergy. In most cases in China, AD facilities need to use multiple feedstocks because of the availability of biowastes in certain areas. However, different biowastes have different biodegradabilities, leading to different AD conversion rates and lower conversion efficiency when two or more different biowastes are directly co-digested. This study used potassium hydroxide (KOH) and liquid fraction, of digestate (LFD) to modify the refractory corn stover (CS) to improve its biodegradability and then be co-digested with readily biodegradable chicken manure (CM). The co-digestion efficiency was expected to increase because of the improved biodegradability of CS by the modifications. The results showed that as compared to untreated CS, 40.83 and 39.38% more biomethane were produced for the co-digestion of CM and CS with KOH and LFD modification, respectively. In addition, the digestion times were reduced by 20 and 30% than the CS + CM group, respectively. The function and response of the microbial community varied with the modifications in population and diversity under mesophilic conditions. Methanosaeta, Methanosarcina, and Methanobacterium were the dominant biomethane-producing archaeal in mono- and co-digestion. Both KOH and LFD modifications could improve the synergistic effect of co-digestion of CS and CM, but LFD modification is recommended because there is no need for extra cost input.