Passion fruit (Passiflora edulis) is a characteristic and advantageous fruit in Guizhou, which is of great significance in poverty relief consolidation and the rural revitalization. However, in recent years, the viral diseases of passion fruit have become increasingly severe, leading to a sharp decline in yield and quality, which thereby seriously constrain industry development of passion fruit. In order to determine the virus species, distribution and compound infestation in the main plantation areas of passion fruit in Guizhou province, a total of 153 samples suspectedly infected by virus were collected from five main plantation orchards of passion fruit in five counties, i.e. Luodian, Congjiang, Rongjiang, Zhenning and Zhenfeng, and the virus detection was carried out by RT-PCR. The results showed that seven viruses were detected from the tested samples, namely East Asian Passiflora virus (EAPV), Telosma mosaic virus (TeMV), Cucumber mosaic virus (CMV), Turnip mosaic virus (TuMV), Passiflora mottle virus (PaMV), Passiflora latene carlavirus (PLV), and Potato virus Y (PVY), among which PVY infection was firstly reported from passion fruit. EAPV was the most prevalent one with infection rate as high as 96.08%, followed consecutively by TeMV (81.70%), CMV (78.43%), TuMV (44.44%), PaMV (26.80%), PVY (24.84%) and PLV (15.03%). In the present case, the distribution of passion fruit viruses in Guizhou province and the diversity of virus sequences were analyzed. Seven viruses were detected in Zhenning, six in Zhenfeng, five in Rongjiang and Congjiang, and three in Luodian. There’s a close identity between the nucleic acid of the seven detected viruses and the corresponding reference sequences (above 95%). Phylogenetic analysis revealed that EAPV, TeMV, PaMV, PLV and TuMV somewhat geographical clustered with passion fruit virus isolated from other provinces in China. CMV and PVY were most closely related to Cucumis melo CMV isolated from Spain and Capsicum annuum PVY isolated from Rwanda respectively, suggesting that the virus sequences diversely varies among the origins in China. A total of 24 types of mixed infection were detected in the main growing areas of passion fruit in Guizhou, and the complex infection rate was as high as 94.77%. The complex infection with 3-5 types predominated in the tested samples, and the combination of EAPV+TeMV+CMV was most frequent among the complex infections among which, EAPV, TeMV and CMV detected ranged from 78.43% to 96.08% in the five counties, somehow reflecting that they were the major viruses to prevent in passion fruit industry of Guizhou province. In addition, a multiplex PCR assay system for EAPV, TeMV and CMV was established in this study, which provides technical support for the rapid detection of related viruses.