Objective:To study the role of neonatal panel detection based on next generation sequencing (NGS) combined with multiplex ligation-dependent probe amplification (MLPA) in the etiological differentiation of neonatal hypotonia.Methods:The clinical characteristics and gene test results of newborns with hypotonia as the main clinical manifestation treated at the Department of Neonatology of Jiangxi Provincial Children's Hospital from March 2017 to March 2021 were retrospectively analyzed.Results:A total of 23 children with hypotonia and feeding difficulties diagnosed by gene tests were included. 17 cases (73.9%) had obvious abnormal appearance, and 11 cases (47.8%) had congenital heart disease (atrial septal defect and/or patent ductus arteriosus). Among the 23 infants, 21 were detected by panel gene, 10 by methylation specific MLPA (MS-MLPA) and 4 by MLPA (SMN1 / SMN2). 14 cases of Prader-Willi syndrome, 4 cases of spinal muscular atrophy, 3 cases of congenital myopathy and 2 cases of Schaaf-Yang syndrome were diagnosed. 11 cases died (47.8%), 9 cases had growth retardation (39.1%), 2 cases had normal growth and development (8.7%), and 1 case survived without detailed information (4.3%). Newborns with unknown etiology and low muscle tone are often complicated with abnormal appearance and congenital heart disease. Neonatal panel combined with MLPA is helpful for accurate diagnosis.Conclusions:The detection of neonatal panel combined with MLPA is cheap, and can provide accurate diagnosis for most newborns with unexplained hypotonia in a short diagnosis cycle, which is conducive to the early formulation of clinical decision-making, and guide the treatment, follow-up and genetic consultation of children.