Abstract: Large-scale storage is very crucial in the development of the biomass industry, due primarily to the seasonal nature of crop harvesting. However, some challenges still remained, such as the self-heating, thermal runaway, and spontaneous combustion during prolonged storage, leading to the low fuel calorific in the biomass storage facilities. Among them, the biomass self-heating can also depend on several factors, for instance, airflow between the biomass stack and the surrounding environment, moisture evaporation and diffusion, the development of microbial communities, low-temperature chemical oxidation and pyrolysis, as well as convective heat transfer between gaseous and solid phases. In this study, a dual-domain model was developed to integrate the turbulence, heat transfer, and moisture transport, thereby considering both within the biomass stack and its external environment. A systematic investigation was made on the various environmental parameters—such as temperature, humidity, and wind speed—together with the initial conditions like temperature, porosity, and chemical composition of the biomass stacks. The influencing factors were finally determined for the self-heating and spontaneous combustion. The results indicated that the turbulent behavior increased at the boundary of the biomass stack with the higher wind velocities at ambient temperature. Additionally, the moisture evaporation from the biomass was impeded under high humidity or low ambient temperatures. The simulation demonstrated that the temperature of the stack initially underwent a rapid increase before stabilizing during storage, where the highest temperature was recorded in the central region. This initial temperature surge was attributed to the thermal energy generated from the degradation of biomass materials after microorganism proliferation. Approximately on the 40th day, the stack temperature attained its peak value of approximately 62°C, after which it decreased gradually. The temperature decline was attributed to the chemical heat produced from the pyrolysis and oxidation of the biomass materials. There was an increasing rate of heat transfer following the initial temperature spike. Ultimately, the stack temperature was stabilized at around 60°C. There was an increase in the initial temperature of the stack from 37 to 47°C, leading to a reduction of 8 days to reach the maximum temperature, along with a decrease of 3°C in the peak temperature. Furthermore, there was a decrease in the porosity of the stack from 0.7 to 0.3 over a storage period of 40 days, which was correlated with a 10°C reduction in the maximum temperature. Furthermore, the self-heating was accelerated into the risk of spontaneous combustion, due to the presence of chemically reactive substances in the biomass feedstock, such as the extractives and hemicellulose. Once the temperature exceeded 80°C, the accumulation of heat within the stack was exacerbated, to seriously increase the spontaneous combustion. The optimal conditions were then clarified for the self-heating and spontaneous combustion of biomass. The correlation between the biomass stack and its external surroundings can greatly contribute to the heat accumulation during storage. The finding can provide a valuable reference to enhance the safety of stack storage in an effective monitoring system.