Although commercial vaccines against porcine circovirus type 2 (PCV2) have been widely implemented globally, PCV2 remains endemic in swine populations, accompanied by ongoing genotype replacement. Meanwhile, the emergence of novel porcine circoviruses (PCVs), including PCV3 and PCV4, has further complicated the prevention and control of porcine circovirus-associated diseases (PCVAD). This study systematically characterized the epidemiological patterns and genetic diversity of PCVs circulating in Eastern China. A total of 739 clinical samples collected between 2010 and 2016 were screened for PCV2. Additionally, 653 samples obtained during 2023–2024 were analyzed using a triplex real-time quantitative PCR (qPCR) assay for the simultaneous detection of PCV2, PCV3, and PCV4. Full-genome amplification and sequencing were subsequently performed on all PCR-positive samples. Epidemiological analysis revealed an overall PCV2 positivity rate of 37.62% during 2010–2016. In the 2023–2024 cohort, the positivity rates for PCV2 and PCV3 were 35.99% and 16.39%, respectively, with a co-infection rate of 10.26%. Notably, no PCV4-positive samples were detected. Phylogenetic analysis demonstrated that PCV2d is the predominant genotype in Eastern China. Furthermore, PCV2g strains were identified in clinical samples for the first time in mainland China, while PCV3b were determined to be the dominant circulating subtype of PCV3. Multiple critical amino acid substitutions were identified within the neutralizing epitopes of the PCV2 Cap protein, and a recombination event involving a PCV2d vaccine strain and a PCV2c reference strain was detected. In contrast, the PCV3 genome exhibited a high degree of genetic conservation. Collectively, these findings expand the molecular epidemiological landscape of PCVs in Eastern China and elucidate the evolutionary dynamics of circulating PCV strains, providing important insights for the development of next-generation vaccines and region-specific PCVAD control strategies.