Defects profoundly affect the magnetic, electronic structure and topological behaviour of intrinsic magnetic topological insulators. Here, we investigate the magnetic, structural stability and topological properties of different Te atomic sites in the intrinsic magnetic topological insulator FeBi2Te4 with Se substitution of the FM-z magnetic order. When Se replaces the outermost site of the septuple layer (the Te atomic layer connected by van der Waals bonds), the Se-Bi bond length formed with its nearest neighbour Bi is drastically shortened and the lattice constant and volume contract accordingly. We speculate that this defect-induced chemical bond enhancement is related to the strong electronegativity of Se over Te. In contrast, the system has lower formation energy, a more stable structure, and enhanced magnetic moment when Se replaces the Te atomic layer inside the septuple layer. Also, we reveal a variety of topological phase transitions due to substitution defects. FeBi2Te4 is considered to belong to the z2×z4 topological classification of higher-order topological insulators with z4=2. The system after Se substitution can be transformed into Weyl semimetals, strong 3D topological insulators, and unknown topological materials without symmetry-base indicators, respectively.