To study the genetic characteristics of primary hemophagocytic lymphohistiocytosis (pHLH) in China, we investigated the genetic data and clinical features of Chinese HLH patients. We retrospectively reviewed the genetic and clinical data of patients with HLH from November 2015 to June 2018. As a result, 26 patients were diagnosed with pHLH. The median age at diagnosis was 2.8 years (range 0.1-13.7 years). The probable overall survival at 12 and 24 months was 87.6% and 62.6%, respectively. Mutations in PRF1 (38.4%) and UNC13D (26.9%) were the most common genetic abnormalities. Furthermore, we identified 19 novel mutations that had not been previously reported and were predicted to likely be pathogenic. In addition to HLH-associated genes, there were 27 other genes identified. Genotype-phenotype analysis showed that patients with disruptive mutations were significantly younger at diagnosis than those with other mutation types (2.9 years vs. 6.4 years, P = 0.036). Familial HLH patients were more prone to central nervous system involvement and seizures compared with other patients (83.3% vs. 37.5%, P = 0.019; 55.6% vs. 12.5%, P = 0.04, respectively). In summary, numerous new mutations in HLH-related genes and other genes were identified in Chinese children with pHLH. Significantly, disruptive mutation types were more likely to be found in younger patients, and familial HLH patients tended to exhibit central nervous system involvement and seizures.