Abstract: The compensated neutron log (CNL) characterizes porosity by measuring hydrogen index (HI). However, its accuracy is not high due to the rock hydrogen content is not completely distributed in the pore fluid and fluid's types are complex. This study aims to determine the main reason for the difference between the measured HI and the formation porosity, thereby deepening the understanding of formation. Using Monte Carlo numerical simulation, multiple factors involved in the HI measurement are analyzed. First, the relationship between the HI and the near-to-far ratio of thermal neutron counting is obtained according to the calibration response of the compensated neutron tool in water-bearing limestone. Second, various factors that cause the difference between HI and formation porosity are obtained on the basis of a comprehensive analysis. The results show that lithology, mineral composition, clay, fluid state, formation water salinity will affect the measurement of HI and make it different from formation porosity. Particularly, high density, high shale content, gas content, and high salinity are the main factors affecting the HI measurement. Overall, this study provides a reference for determining formation porosity and identifying oil and gas through neutron data in the future.