Chromosomal microarray analysis (CMA) is a technique for screening numerical and structural abnormalities of chromosomes at the whole genome level. It is a routine tool for pediatric and prenatal genetic diagnoses. It has also been applied to investigate the genetic etiologies of miscarriages. In our study, we used the CMA technology to analyze the chromosomal variations of fetuses from miscarriages at the whole genome level, and to evaluate its clinical applications in studies of miscarriages. The CMA analyses were performed on 2600 miscarriage specimens, of which 2505 specimens (96.35%) were successfully analyzed. Among them, 1021 specimens were analyzed with CytoScan Optima chip; 1211 specimens were analyzed with CytoScan 750K chip; and 273 cases were analyzed with CytoScan HD chip. Chromosomal abnormalities were identified in 967 specimens (38.6%) by these 3 kinds of chips, of which 506 specimens (50.00%) were detected with CytoScan Optima chip; 388 specimens were detected by CytoScan 750K chip (32.00%); and 73 cases (26.74%) were detected in CytoScan HD chip. Among the 967 cases of chromosomal abnormalities, 801 cases (82.83%) were numerical chromosomal abnormalities; 94 cases (9.72%) were structural abnormalities; 56 cases (5.79%) were mosaicisms; and 16 (1.65%) were regions of homozygosity. Our research suggests that CMA is a reliable, robust, and high-resolution technology for genetic diagnosis of miscarriage in clinical practice, which can also provide results as guidance for the risk assessment of assisted fertility.