Bacillus thuringiensis (Bt) protein expressed by genetically modified (GM) crops is released into the soil ecosystem, where it accumulates for a long time; therefore, degradation of Bt protein has gained increased attention for environmental risk assessments. A first-order kinetic model (Y = ae−b*X) is usually used to evaluate the degradation of Bt proteins, including Bt-Cry1Ab and Bt-Cry1Ac; this has some limitations regarding the precise fitting and explanation of the influence of various factors on Bt protein degradation in the later stage. Therefore, to amend these limitations, we report a new degradation model Y = Y0 + ae−b*X. The effects of soil temperature, water content, soil types, and soil sterilization on the degradation of Bt-Cry1Ah protein in soil were estimated in a 96d long laboratory study using a GM maize leaf–soil mixture. The results showed that the Bt-Cry1Ah protein degraded rapidly in the early stage and then slowly in the middle and late stages. Temperature was identified as the key factor affecting the degradation of Cry1Ah protein—a relatively higher temperature favored the degradation. The degradation rate of Cry1Ah protein was the fastest when the water content was 33 and 20% in the early and later stages, respectively. The soil types had a significant effect on the degradation of Cry1Ah protein. Moreover, soil sterilization slowed down the rate of protein degradation in both the early and later stages. In conclusion, the model Y = Y0 + ae−b*X established in this study provided a more robust model for exploring and simulating the degradation of Bt protein in soil growing GM crops and overcame the shortcomings of the Y = ae−b*X model. The findings of this study enriched the understanding of Bt protein degradation in soil ecosystems. They would be helpful for evaluating the environmental safety of GM crops.