Corn stover dry matter loss effects variability for biofuel conversion facility and technology sustainability. This research seeks to understand the dynamic mechanisms of the thermal system, organic matter loss, and microbial heat generation in corn stover storage operations through system dynamics, a mathematical modeling approach, and response analysis to improve the system performance. This study considers epistemic uncertainties including cardinal temperatures of microbial respiratory activity, specific degradation rate, heat evolution per unit substrate degraded, and thermal conductivity in corn stover storage reactors. These uncertainties were managed through calibration, a process of improving the agreement between the computational and benchmark experimental results by adjusting the parameters of the model. Model calibration successfully predicted the temperature of the system as quantified by the mean absolute error, 0.6 • C, relative to the experimental work. The model and experimental dry matter loss after 30 days of storage were 5.1% and 4.9 ± 0.28%. The model was further validated using additional experimental results to ensure that the model accurately represented the system. Model validation obtained a temperature mean absolute relative error of 0.9 ± 0.3 • C and dry matter loss relative error of 3.1 ± 1.5%. This study presents a robust prediction of corn stover storage temperature and demonstrates that an understanding of carbon sources, microbial communities, and lag-phase evolution in bi-phasic growth are essential for the prediction of organic matter preservation in corn stover storage systems under environment's variation.