Two novel pretreatment methodologies, namely, ammonia recyclable percolation (ARP) and liquid ammonia (LA), were introduced for corn stover (CS) in the present study to enhance methane production. In the past, ARP and LA fractionation were mostly utilized as pretreatments to enhance the enzymatic digestibility of CS to produce fermentable sugars and ethanol. The CS was pretreated by the ARP and LA pretreatment methods at two concentration levels, and their effects on the lignocellulosic characteristics and resultant methane enhancement were evaluated. All pretreatments were found to be significant (P < 0.05) in enhancing xylan solubilization, lignin removal, and methane production. The ARP-2 pretreatment was found to be the optimum pretreatment with 50.69%, 44.15%, and 57.52% xylan removal, lignin removal, and C/N reduction, respectively, as compared to the untreated CS. To optimize the most suitable pretreatment for CS, process stability and biochemistry parameters such as total volatile fatty acids (TVFA), chemical oxygen demand (COD), pH, and alcohol production were deeply monitored during the anaerobic digestion period.