The growing demand to lower greenhouse gas emissions and transition from fossil fuels, has put methanol in the spotlight. Methanol can be produced from renewable sources and has the property of burning almost soot-free in compression ignition (CI) engines. Consequently, there has been a notable increase in research and development activities directed towards exploring methanol as a viable substitute for diesel fuel in CI engines. The challenge with methanol lies in the fact that it is difficult to ignite through compression alone, particularly in low-load and cold start conditions. This difficulty arises from methanol's high octane number, relatively low heating value, and high heat of vaporization, collectively demanding a considerable amount of heat for methanol to ignite through compression. Previous studies have addressed the use of a pilot injection in conjunction with a larger main injection to lower the required intake air temperature for methanol to combust at low loads. While this approach has shown promise, there has been limited testing and documentation of how the pilot injection should be configured for optimal results. The research presented in this study explored combinations of six different dwell times, between the pilot and the main injections, with three different pilot injection lengths. The findings demonstrated that a dwell time ranging from 15 to 20 CAD, combined with a pilot injection of 250 to 375 μs, can lead to highly stable combustion at an intake air temperature more than 30°C lower than that required when not using a pilot injection. Additionally, these configurations resulted in a five percentage point increase in efficiency, comparable CO and HC emissions, and significantly reduced NOx emissions. In summary, the study highlighted the effectiveness of using a specific pilot injection in enhancing combustion stability, efficiency, and emissions during low-load methanol compression ignition operation.