Feline coronavirus (FCoV) is the causative agent of feline infectious peritonitis and diarrhea in kittens worldwide. In this study, a total of 173 feline diarrheal fecal and ascetic fluid samples were collected from 15 catteries and six veterinary hospitals in southwest China from 2017 to 2020. FCoV was detected in 80.35% (139/173) of the samples using the RT-nPCR method; these included infections with 122 type I FCoV (87.8%) and 57 type II FCoV (41%). Interestingly, 51 cases (36.7%, 51/139) had co-infection with types I and II, the first such report in mainland China. To further analyze the genetic diversity of FCoV in southwest China, we amplified 23 full-length spike genes, including 18 type I and five type II FCoV. The 18 type I FCoV strains shared 85.9%–100% nucleotide sequence identities between one another and the five type II FCoV strains shared 97.4%–98.9% nucleotide sequence identities between one another. This result suggests that the N-terminal domain (NTD) of 23 FCoV strains showed a high degree of variation (73.6%–80.3%). There was five type I FCoV strains with two aa insertions (159HL160) in the NTD region. In addition, 18 strains of type I FCoV belonged to the Ie cluster, and five strains of type II FCoV were in the IIb cluster based on phylogenetic analysis. It is worth noting that five type I FCoV strains also had recombination in the NTD, and the recombination region was 135–625 nucleotides of the S gene. This study constitutes a systematic investigation of the current infection status and molecular characteristics of FCoV in southwest China.