The long-term performance of steel-spontaneous combustion coal gangue aggregate concrete (S-SCGAC) composite slabs was investigated in this study. Shrinkage tests were performed on 20 groups of specimens to quantify the effects of the replacement ratio (rc) of spontaneous-combustion coal gangue aggregate (SCGA) and humidity boundary conditions on the shrinkage of SCGAC specimens. A non-uniform shrinkage model for S-SCGAC composite slabs was further proposed. A long-term performance design method of S-SCGAC composite slabs was put forward by using ABAQUS software to establish a finite element model of the long-term performance of composite slabs considering the influence of non-uniform shrinkage, and to quantify the influence of parameters on the long-term performance. The results showed that the shrinkage deformation of SCGAC specimens increased significantly with increasing rc, and humidity boundary conditions were found to have a significant effect on the shrinkage performance of SCGAC specimens. The exposed surface shrinkage of the concrete under single-sided humidity transfer conditions was 1.01–1.09 times that under double-sided humidity transfer conditions, and the sealed surface shrinkage of the concrete under single-sided humidity transfer conditions was only 5.4%–14.4% of that under double-sided humidity transfer conditions. The long-term deflection of S-SCGAC composite slabs proved to be significantly affected by rc. When rc increased from 0% to 100%, the long-term deflection of the composite slab increased on average by 67.2%. The long-term deflection calculation method considering the effect of non-uniform shrinkage was shown to yield promising prediction results.