This study investigates the enhancement of biogas production from hemp biomass residue (HBR) through hydrothermal pretreatment and co-digestion with cow manure (CM). Hydrothermal pretreatment at 200 °C for 15 min significantly improved the methane yield from 311.5 to 434.3 mL-CH4/g-VSadded (p ≤ 0.05) from HBR at 10% total solids (TS) loading, a 39% increase. Co-digestion with CM at an optimum ratio of 80:20 further increased the methane yield (738.7 mL-CH4/g-VSadded), representing a 70% improvement over pretreated HBR alone and a 137% increase compared to untreated HBR. Microbial community analysis revealed the dominance of Methanosaeta, comprising 83–93% of archaeal genera across samples. Gene expression analysis showed acetoclastic methanogenesis as the dominant pathway, accounting for 80% of methanogenesis sequences. Hydrogenotrophic methanogenesis and CO2 reduction with H2 pathways contributed 10% each. The optimized process achieved a biodegradation efficiency of 94% for hydrothermally pretreated HBR, compared to 68% for untreated HBR. Mass balance analysis demonstrated that combining hydrothermal pretreatment with anaerobic digestion increased biogas yield from 79% for untreated HBR to 86% for pre-treated HBR (PHBR) co-digested with CM. Integrating hydrothermal pretreatment and co-digestion enhances biogas production from lignocellulosic agricultural residues, contributing to sustainable waste management and renewable energy production.