The process of animal regeneration involves the organization of specific cell types in both space and time. This requires precise information about the position of cells to guide the recovery of cell landscapes, which is a major challenge in understanding the anatomy of four-dimensional time and space. Here, our reconstruction of single-cell resolved Planarian Regenerative Interactive Spatiotemporal Transcriptomic Atlas in four Dimensions (PRISTA4D) in homeostatic and regenerating planarians has revealed the genes involved in the spatial and cell-type resolution response to regeneration. The PRISTA4D atlas provides insight into the organizational essences of positional gradients during regeneration and highlight the potential of 4D-ST to chart the multi-scale biological processes.