Deposit formation remains a critical challenge in the utilization of palm oil biodiesel due to its high viscosity, low volatility, and dominance of saturated fatty acid methyl esters (FAME). This study investigates the effect of methanol addition on deposit formation behavior of palm oil biodiesel using a Hot Surface Deposit Test (HSDT), with a focus on linking molecular composition, thermophysical properties, and evaporation-driven deposit mechanisms. Biodiesel methanol blends with methanol contents ranging from 5% to 25% were characterized using GCMS, density, viscosity, and heating value measurements. Deposit formation was evaluated under hot surface temperatures between 230 °C and 290 °C. GCMS results revealed that methanol addition systematically shifted the FAME composition from saturated methyl esters toward unsaturated species, particularly methyl oleate and methyl linoleate. This compositional change was accompanied by a significant reduction in density up to 2.3% and viscosity over 30%, enhancing droplet atomization and evaporation characteristics. The heating value of the blends decreased with increasing methanol content, leading to reduced thermal cracking intensity during droplet–surface interaction. HSDT results demonstrated a substantial reduction in deposit area with increasing methanol fraction and surface temperature, indicating a transition from a liquid-film-dominated to an evaporation-dominated deposit formation regime. The findings highlight that deposit mitigation in palm oil biodiesel can be effectively achieved through fuel formulation strategies that enhance evaporation kinetics rather than relying solely on antioxidant additives or engine hardware modifications. Methanol is shown to function as an evaporation-enhancing additive that suppresses deposit formation by synergistically modifying molecular composition, physical properties, and thermal behavior of biodiesel.