A global outbreak of infections due to Mycobacterium chimaera has been linked to the LivaNova (formerly Sorin) 3 T heater-cooler units (HCUs). We performed a study to investigate M. chimaera from HCUs in China. Water samples were collected from all 3 T HCUs (n = 5) at our hospital in May 2017. Mycobacteria isolates were subjected to genome sequencing using the HiSeq X10 Sequencer. Species were identified based on average nucleotide identity with M. chimaera type strain DSM 44623T. Paired-end reads of all M. chimaera genomes were retrieved from the SRA database and, together with our isolates, were mapped against the chromosome of M. chimaera reference strain ZUERICH-1 to call SNPs. Mycobacteria grew from three HCUs manufactured in 2009 but not from the two in 2016. The three isolates were identified as M. chimaera and differed from each other by 4 to 6 SNPs, and from ZUERICH-1 by 7 to 10 SNPs. The three isolates belonged to the subgroup 1.1 and were most closely related to strains of the subgroup 1.1 from HCUs or patients in Europe, Australia/New Zealand and USA, suggesting the same common source. This is the first report of M. chimaera from HCUs in China.