This work evaluates how varying the methanol energy share affects efficiency, combustion behavior, and pollutant formation in a methanol–diesel-fueled Reactivity-Controlled Compression Ignition (RCCI) engine. A comprehensive experimental campaign was performed under both constant and dynamically varying operating conditions, covering engine speeds from 1400 to 2000 rpm and load levels ranging between 25% and full load. The methanol substitution rate (MSR) was systematically adjusted from 0% to 40% to assess its influence on combustion and emission performance. The findings demonstrate that a higher methanol contribution significantly improves brake thermal efficiency, with gains reaching approximately 14% at elevated load conditions. However, excessive methanol addition slightly increases cycle-to-cycle variations, indicating a modest reduction in combustion stability. Changes in MSR were also observed to strongly influence gaseous and particulate emissions. Compared with conventional diesel operation, increasing methanol fraction led to notable reductions in nitrogen oxides and particulate matter, while carbon monoxide levels exhibited sensitivity to combustion phasing and mixture reactivity. Analysis of the measured data revealed that NOx emissions declined by nearly 30–50% at higher methanol fractions, and particulate emissions remained considerably lower than those produced by diesel-only combustion. In addition, vibration-based virtual sensing combined with time–frequency domain analysis showed that methanol enrichment modifies heat release characteristics and pressure rise rates, which subsequently alters engine structural vibration responses and emission trends. Exergy assessment further indicated that a methanol substitution ratio of approximately 30% minimizes irreversibility losses, signifying superior energy utilization efficiency and the most thermodynamically favorable combustion condition within the tested range.