Structural properties of biomaterials play critical roles in guiding cell behaviors and influence the immune response against them. In this study, we fabricated electro-spun membranes with three types of surface topography (Random, Aligned, and Latticed). The aligned membranes showed immunomodulatory ability, and led to faster wound healing, reduced fibrotic response and enhanced regeneration of cutaneous appendages. Based on that, we performed single-cell RNA sequencing analysis on cells of wounded mouse skin in the presence/absence of the Aligned scaffold. We identified 45 cell populations. Keratinocytes, fibroblasts, and immune cells including neutrophils, monocytes, macrophages, dendritic cells, and T cells showed diverse cellular heterogeneity. We found more inner root sheath cells (anagen-related) in the Aligned group, which corresponded to the improved regeneration of hair follicles in the presence of scaffold. The immune microenvironment around the biomaterial involved intricate interplay of immune cells from both innate and adaptive immune system. Immune responses in tissue around scaffold significantly differed from that of saline control. In aligned samples, infiltrated macrophages and neutrophils were reduced, whereas more effector T cells were recruited. The time course of immune response might be advanced towards an adaptive immunity-dominant stage by scaffolds.