Objective　To explore the diagnosis and treatment of atypical severe combined immunodeficiency disease (SCID). Methods　The clinical data of atypical SCID in 7 children with IL2RG, JAK3, and RAG1 mutations were reviewed and analyzed from September 2012 to June 2017. Results　In 7 cases (6 males and 1 female), there were 5 infants, 1 toddler and 1 school-age child. Cases 2, 4, and 6 were classic SCID clinical phenotypes. Cases 1, 3, 5, 7 were atypical SCID clinical phenotypes. Case 6 were diagnosed with Omenn syndrome. Cases 2, 5 were classic SCID immune phenotypes, cases 1, 3, 4, 6, 7 were atypical SCID immune phenotypes, and case 1 had maternal chimera. The next generation sequencing indicated that case 1 had a compound heterozygous JAK3 mutation with c.3097-1G>A/ c.946-950GCGGA>ACinsGGT. Cases 2, 3, and 4 had IL2RG mutations, with c. 865C>T/ p.R289X, c.664C>T/R222C, 52delG, respectively. Case 5 had JAK3 mutations with c.2150A>G/p.E717G and c.1915-2A>G. Sanger sequencing indicated that case 6 had a RAG1 mutation of complex heterozygosity with c.994C>T/p.R332X and c.1439G>A/p.S480N. Case 7 had homozygous RAG1 mutation with c.2095C>T/p.R699W. Conclusion　Under certain conditions, gene mutation can lead to atypical clinical and/or immune phenotypic SCID.