Enterovirus G (EV-G) is an important enteric pathogen widely circulating in swine populations and is characterized by considerable genetic diversity and recombination potential. In recent years, recombinant EV-G strains carrying exogenous papain-like cysteine protease (PLCP) gene insertions have been increasingly reported; however, their genotype distribution and molecular characteristics in major pig-producing regions remain poorly understood. In this study, 356 clinical samples collected from Guangxi, southern China, between 2020 and 2025 were screened for EV-G, and 13 representative strains were subjected to whole-genome sequencing and sequence analysis. The overall EV-G positivity rate in Guangxi was 20.51% (73/356). Phylogenetic analysis showed that the 13 Guangxi EV-G strains were mainly classified into three genotypes, G1, G2, and G8, with G1 being the predominant genotype. Notably, PLCP gene insertions of 573–642 nt were identified at the 2C/3A junction in seven strains belonging to three distinct genotypes, G1, G2, and G8, demonstrating the cross-genotype distribution of PLCP insertions within a single geographic region. Phylogenetic analysis of the PLCP sequences demonstrated that all Guangxi-derived PLCP sequences clustered within the EV-G-PLCP clade and were clearly separated from the torovirus PLCP clade. Recombination analysis retained three potential recombination events with clearer combined support from RDP4 and SimPlot analyses, involving Guangxi strains GX3008, GX3022, and GX4292. Selection pressure analysis showed that the VP1 gene was overall under negative selection. Collectively, these findings demonstrate the co-circulation of multiple EV-G genotypes, the cross-genotype distribution of PLCP insertions, and the presence of potential recombination events in Guangxi. This study provides new evidence for understanding the genetic diversity, genomic plasticity, and regional molecular characteristics of EV-G, and also provides an important basis for future PLCP-related functional studies and continued EV-G surveillance.