The human mastadenovirus C (HAdV-C) cause respiratory infections in children. Homologous recombination was clearly involved in the molecular evolution of HAdV-A, B, and D, but little is known about the molecular evolution of HAdV-C. From 2000 to 2016, 201 HAdV-C strains were collected from nine provinces covering six administrative regions of mainland of China via 3 existing surveillance programs, namely the febrile respiratory syndrome surveillance, the acute flaccid paralysis surveillance, and the hand, foot, and mouth disease surveillance system. The genes coding for the capsid protein (penton base, hexon, and fiber) of 201 HAdV-C strains were sequenced and compared with representative sequences publicly available. In addition, the whole genome sequence of 24 representative strains of HAdV-C was generated for further recombination analysis. Phylogenetic analysis of the penton base sequences of HAdV-C revealed six genetic groups (labelled as Px1-6), which showed that the penton base had more variation than previously thought. Based on the penton base, hexon, and fiber gene sequences, 16 new genetic patterns of HAdV-C circulating in mainland of China were identified in this study. Whole genome sequence analysis revealed frequent recombination events among HAdV-C genomes. This study is highly beneficial for case classification, tracking the transmission chain, and further epidemiological exploration of HAdV-C-related severe clinical diseases in the near future. Our data demonstrated that multiple newly divergent HAdV-C co-circulated across mainland China during the research period.