Vortex pinning is a crucial factor that determines the critical current of practical superconductors. However, the understanding of its underlying mechanism has long been phenomenological without a clear microscopic description. Here using high-resolution scanning tunneling microscopy, we studied single vortex pinning induced by point defect in layered FeSe-based superconductors. We found the defect-vortex interaction drives low-energy vortex bound states away from EF, resulting a mini gap which effectively lowered the energy of vortex and caused the pinning. By measuring the local density-of-states, we directly obtained the elementary pinning energy and estimated the pinning force through the spatial gradient of pinning energy. The results align with the bulk critical current measurement. We further show that a general microscopic quantum model with considering defect-vortex interaction can well capture our observation. It indicates the local pairing near pinned vortex core is actually enhanced, which is beyond the traditional understanding that non-superconducting regions pin vortices. Our study thus revealed a general microscopic mechanism of vortex pinning in superconductors.