Porcine epidemic diarrhea virus (PEDV), an enteric coronavirus, has become the major causative agent of acute gastroenteritis in piglets since 2010 in China. Given a raised interest in the mutation and recombination of viral genomes, the genetic and antigenic characteristics of PEDV should be continuously investigated. In the current study, 91 complete spike (S) gene sequences were obtained from PEDV positive samples collected from17 provinces in China from March 2020 to March 2021. A phylogenetic analysis showed that 92.3% (84 out of 91) of the identified strains belonged to GII subtype, while 7.7 % (7 out of 91) were categorized as S-INDEL like strains and grouped within GI-c clade. Based on a recombination analysis, six of S-INDEL like strains were recombinant strains originated from S-INDEL strain FR/001/2014 and vaccine strain AJ1102. In addition, PEDV variant strains carrying novel insertions (360QGRKS364 and 1278VDVF1281) in the S protein were observed. Furthermore, the deduced amino acid sequences analysis for the S protein showed that multiple amino acid substitutions in the neutralizing domain (COE) and three neutralizing epitopes (S1 ^A, SS6, 2C10) were found as compared with the vaccine strains (CV777 and AJ1102). The recombination of field and vaccine strains, along with variation of antigenic epitopes, might affect the virulence and antigenicity of PEDV, thus resulting in a failure of immunization. In conclusion, these data provide novel molecular evidences on the epidemiology and molecular diversity of PEDV in 2020–2021. This information may help design a strategy for controlling and preventing the prevalence of PEDV variant strains in China.