MSCsDB is a publicly available biological database that facilitates the analysis of single-cell RNA sequencing expression data for mesenchymal stem cells (MSCs) across five different tissues and 26 samples. The database utilizes a standardized processing pipeline and offers a comprehensive evaluation of the integrated data to provide a broad phenotypic landscape overview and data query. The database also incorporates several customizable functions, such as clustering and automated annotation, pathway enrichment, copy number variation analysis, pseudotime analysis, and transcription factor regulatory network mapping, through the utilization of various Python packages such as Scanpy, InferCNVpy, pySCENIC, as well as R packages such as ClusterProfiler, CopyKAT, and Seurat.