H3N2 feline influenza virus (FIV) and canine influenza virus (CIV) are very common in cats and dogs. Due to the ability of influenza virus to spread across hosts and frequent contact between pets and people, there exist huge public health problems. In this study, we collected H3N2 CIV and FIV genomes from 2006 to 2019 from NCBI and analyzed the evolutionary dynamics and molecular variation using a series of phylogenetic analysis methods. Results indicated that H3N2 FIVs was closely related to CIVs with high posterior probability and CIVs and FIVs have certain regional characteristics. However, compared with previous studies, the significance of geographical structure correlation decreased. Furthermore, we also found that the intrasubtypic reassortment between FIVs and CIVs were common during epidemics. Integrated analysis was also performed for different selection pressure acting on HA (566 codons), NA (469 codons), M1 (252 codons) and M2 (97 codons) proteins. 1 HA, 2 NA, 3 M1 and 2 M2 sites were found under positive selection. We subsequently performed evolutionary dynamics of H3N2 CIV. The results indicated that the tMRCA of CIV H3N2 may have occurred earlier than indicated in a previous study. The Bayesian skyline plot analysis in this study showed the period of divergence of major H3N2 CIVs segments occurred between 2008 to 2010. Notably, according to our research, the PB1 has experienced two divergence periods (2006-2008 and 2009-2011).