Osteogenesis imperfecta (OI) is a serious genetic bone disorder characterized by congenital low bone mass, deformity and frequent fractures. Type XV OI is a moderate to severe form of skeletal dysplasia caused by WNT1 mutations. In this cohort study from southern China, we summarized the clinical phenotypes of patients with WNT1 mutations and found the proportion of type XV patients was around 10.3% (25 out of 243) with diverse phenotypic spectrums. Functional assays indicated that mutations of WNT1 significantly impaired its secretion and effective activity, leading to moderate to severe clinical manifestations, porous bone structure and enhanced osteoclastic activities. Analysis of proteomic data from human skeleton indicated that the expression of SOST was dramatically reduced in type XV patients. Single-cell transcriptome data generated from human tibia samples revealed aberrant differentiation trajectory of skeletal progenitors and impaired maturation of osteocytes, resulting in excessive CXCL12+ progenitors and abnormal cell populations with adipogenic characteristics. The integration of multi-omics data from human skeleton delineates how WNT1 regulates the differentiation and maturation of skeletal progenitors, which will provide a new direction for the treatment strategy of type XV osteogenesis imperfecta and relative low bone mass diseases such as early onset osteoporosis. Overall design: With patients’ consents, the skeletal tissues were collected after tibia osteotomies from a patient (male, 8-year-old) carrying compound heterozygous mutations on WNT1 (c.C371T, p.T124M and c.G620A, p.R207H), and a patient with leg-length-discrepancy (male, 7-year-old) (Figure S1). The control patient was diagnosed with Proteus syndrome, with genetic testing confirming a pathogenic mutation (c.49G>A, p.E17K, sample frequency 13.3%) on AKT1. Single-cell RNA-seq reads happened to cover this region, where it showed a frequency of 6.3% (c.49G>A, 5 out of 79). Although it is not a perfect control, given the relatively normal bone density and histology, we assumed that it could be a useful reference for type XV OI.