The variation in roof structure induced by changes in bedrock thickness exerts a direct influence on the stress distribution within lower strata, consequently governing the stability of roadway surrounding rock. To investigate the impact of bedrock thickness variations on overburden fracture behavior and stress evolution in deep-buried thick loose layers, a numerical simulation model of an unequal-thickness bedrock working face was developed using discrete element numerical simulation software. This model was utilized to conduct a systematic investigation into the fracture characteristics of the overburden, displacement characteristics, and stress evolution during the mining process. The results demonstrate that as the working face advances and bedrock thickness progressively increases, several significant changes occur: the caving interval of the immediate roof extends; the degree of fragmentation, overall separation, and subsidence of the caving rock layer above the goaf gradually diminish; the peak stress at the working face shifts deeper into the coal wall; and the stress influence zone expands. Through the establishment of a mechanical model of the key strata, a fracture formula for the overburden was derived, elucidating the fracture mechanics of bedrock with varying thicknesses. A combined support measure tailored to varying bedrock thicknesses has been developed. Practical applications have demonstrated the technology’s effectiveness in maintaining roadway stability, offering valuable guidance for safe and efficient mining operations under comparable geological conditions.