Atypical porcine pestivirus (APPV) is one major causative agent of congenital tremor (CT) type A-II. In this study, the geographical distribution and genetic characteristics of APPV strains in China were established. To date, APPV has been detected in at least ten provinces/regions of China. Genetic variability analysis showed that NS3 genes were highly conserved among Chinese APPV strains, while NS5A-, Npro-, and Erns-encoding genes were highly variable. Phylogenetic analysis revealed that all of the reference strains could be classified into 3 genotypes (1-3) and 7 subgenotypes (1.1-1.7). The Chinese APPV strains were assigned to all 3 genotypes and to 5 subgenotypes (1.2 and 1.4-1.7) of genotype 1. Amino acid insertions/deletions in nonstructural proteins, including NS3, NS5A, and NS5B, could only be found in Chinese APPV strains. Among the three envelope glycosylation proteins (Erns, E1, and E2), Erns was the most heavily glycosylated protein, and the N-glycosylation sites of E2 in different APPV strains showed apparent correlations with genetic types. Furthermore, a novel APPV strain named China/HeN01/2018 belonging to genotype 2 was identified in Henan Province. It was then isolated and successfully propagated in embryonic porcine kidney epithelial cells (SPEV cells). This study provides updated information to better understand the divergence of APPV strains in China. This first successful isolation of a Chinese APPV strain provides a research foundation for future studies.