In order to improve the performance of methane production from agro-waste, a batched four-stage–two-phase anaerobic digestion (4S2P-AD) system was designed to combine the advantages of both anaerobic co-digestion (co-AD) and two-phase AD. The initial separation of two phases was performed using rice straw (RS) as a feedstock in acidogenic phase and cow manure (CM) in methanogenic phase at low inoculum/substrate (I/S) ratios of 0.5 and 0.2 and a high organic loading of 60 g volatile solid (VS)/L. The periodic round-trip reflux of leachate during the 4S2P-AD process facilitated re-inoculation throughout the four stages. The results showed that this round-trip reflux also dispersed toxic ammonia, balanced the carbon/nitrogen ratio, unified the microbial community structure, and led to the selection of Methanosarcina (relative abundance > 80%) as the dominant methanogens. With the abilities to overcome volatile fatty acid accumulation, shorten lag times, improve biodegradability, and foster synergistic effects, it was verified that the 4S2P-AD process can maintain efficient and stable methanogenesis from high-solid lignocellulosic feedstock. The averaged methane production throughout the four stages of 4S2P-AD was 234 mL/g VS. This result is 96% higher than the averaged methane production obtained from the four one-step AD groups using mono-feedstock, and 91% higher than that obtained using co-feedstock. This study provides a scientific reference for the development of new processes of bio-methane production from agro-waste with a high fermentation capacity and stability in the future.