Seneca Valley virus (SVV) is a novel Picornaviridae that is closely associated with porcine idiopathic vesicular disease (PIVD). Here, a novel SVV strain (CH-GX-01-2019) was detected and isolated from swine in Guangxi Province, China. The complete genomic sequence of CH-GX-01-2019 exhibited 93.3–98.9 % identify with other SVV isolates at the nucleotide level. CH-GX-01-2019 showed the highest level of similarity (98.9 %) with Vietnamese strains. And CH-GX-01-2019 exhibited two consecutive amino acid mutations in VP1 gene. Phylogenetic analysis based on the complete genome and the VP1 gene showed that Chinese SVV isolates can be divided into three clusters. We analyzed the geographical distributions of SVV strains in China and found that the epidemiology of SVV in China is complicated; most strains are distributed predominantly in south and central China. Between 2015 and 2019, the dominant epidemic SVV isolates in China have changed from clusters 1 and 3 to cluster 2. CH-GX-01-2019 (cluster 3) is a recombinant strain from Colombia-2016 (cluster 2) and HB-CH-2016 (cluster 1). Our findings will enhance our understanding of the prevalence and genetic variation of SVV in the swine herds of China and provide important insights into the molecular epidemiology of SVV.