Objective: To explore the clinical characteristics of newborns infected with SARS‐CoV‐2 Omicron Subvariants BF.7 and BA. 5.2, and to compare the clinical characteristics of newborns infected with different subtypes of coronavirus strains. Methods: The newborns suspected of SARS‐CoV‐2 infection admitted in December 2022 were selected for viral nucleic acid detection and typing. The clinical characteristics, laboratory examination and prognosis of the newborns with nucleic acid positive were analyzed. The clinical characteristics of different subtype virus strains in newborns were compared. Results: There were 43 newborns with positive SARS‐CoV‐2 nucleic acid test, 2 asymptomatic infections, 37 mild infections and 4 severe infections. The mild cases all showed symptoms of upper respiratory tract infection, of which 3 cases were accompanied by gastrointestinal symptoms; Three severe case showed respiratory symptoms, and the other one showed gastrointestinal symptoms. The hospital stay of newborns with symptomatic infection was 5.0 (4.0, 7.0) days. All cases were cured and discharged. Most newborns were followed up without abnormal clinical manifestations after discharge. The whole gene sequencing of 33 samples with high viral load showed that 14 cases were Omicron BF.7 subtype and 19 cases were BA.5.2 subtype. In BA. 5.2 cases, 2 cases were severe, 17 cases were mild, and 4 cases had gastrointestinal symptoms, while in BF. 7 group, 2 cases were asymptomatic, 12 cases were mild, and no cases showed gastrointestinal symptoms. There was no significant difference between the two groups in terms of age of onset, hospital stay, incidence of fever, cough, convulsion, and laboratory examination (P＞0.05). Conclusions: Neonates infected with SARS‐CoV‐2 Omicron variant are mainly characterized by mild symptoms and respiratory symptoms, and a few of them are characterized by gastrointestinal symptoms. After infection with BA.5.2 subtype, some children have gastrointestinal symptoms, and a few children have severe clinical symptoms. Whether the incidence of gastrointestinal symptoms and severe diseases caused by Omicron variant BA. 5.2 is higher than that caused by BF. 7 requires further large sample study.