Background: Congenital myasthenic syndromes (CMS) are a group of inherited disorders caused by genetic defects in neuromuscular junction. Mutations in CHAT, encoding choline acetyltransferase, cause congenital myasthenic syndrome with episodic apnea (CMS-EA), previously named familial infantile myasthenia. Up to now, there was no compound heterozygous exons deletion and missense variant described, and there was no Chinese mainland report. Objective: Investigate the clinical and genetic features of CMS-EA caused by gene mutation of CHAT in China. Methods: The clinical data of 2 patients with CMS-EA were collected, the clinical features and gene mutation characteristics were analyzed, and the patients were followed-up for therapeutic efficacy. Results: The two patients had their age of onset soon after birth and 3 months respectively, and were admitted to the PICU due to dyspnea, cyanotic episodes that required intubation. One died when 10 months old, while the other had a good effect on pyridostigmine. Both cases were negative for anti-AChR, anti-acetylcholinesterase, anti-MuSK antibodies. Neostigmine test was negative and suspiciously positive respectively. Cranial MRI of both cases showed brain atrophy-like change. Genetic testing showed compound heterozygous deletions (exon 4, 5, 6) and pathogenic variant c.914T>C (p.I305T) in CHAT, compound heterozygous variants c.1007T>C (p.I336T) and c.64C>T (p.Q22X) in CHAT, respectively. Conclusion: CMS-EA is a treatable rare disease, early treatment with pyridostigmine is helpful to the improvement of clinical symptoms and prognosis.