This study assessed the impact of organic loading rate (OLR) on methane (CH4) production in the anaerobic co-digestion (AcoD) of sugarcane vinasse and molasses (SVM) (1:1 ratio) within a thermophilic fluidized bed reactor (AFBR). The OLR ranged from 5 to 27.5kg COD.m-3.d-1, with a fixed hydraulic retention time (HRT) of 24h. Organic matter removal varied from 56 to 84%, peaking at an OLR of 5kg COD.m-3.d-1. Maximum CH4 yield (MY) (272.6 mL CH4.g-1CODrem) occurred at an OLR of 7.5kg COD.m-3.d-1, while the highest CH4 production rate (MPR) (4.0L CH4.L-1.d-1) and energy potential (E.P.) (250.5 kJ.d-1) were observed at an OLR of 20kg COD.m-3.d-1. The AFBR exhibited stability across all OLR. At 22.5kg COD.m-3.d-1, a decrease in MY indicated methanogenesis imbalance and inhibitory organic compound accumulation. OLR influenced microbial populations, with Firmicutes and Thermotogota constituting 43.9% at 7.5kg COD.m-3.d-1, and Firmicutes dominating (52.7%) at 27.5kg COD.m-3.d-1. Methanosarcina (38.9%) and hydrogenotrophic Methanothermobacter (37.6%) were the prevalent archaea at 7.5kg COD.m-3.d-1 and 27.5kg COD.m-3.d-1, respectively. Therefore, this study demonstrates that the organic loading rate significantly influences the efficiency of methane production and the stability of microbial communities during the anaerobic co-digestion of sugarcane vinasse and molasses, indicating that optimized conditions can maximize energy yield and maintain methanogenic balance.