Viral diseases pose a serious threat to pumpkin cultivation, which is an important cucurbitaceous vegetable crop. Recently, multi-virus mixed infections in plants have been continuously detected and reported. However, studies on mixed virus infections in pumpkins are limited. Through metavirome and polymerase chain reaction (PCR) analysis, we found that pumpkins exhibiting severe viral symptoms were co-infected with squash leaf curl China virus and tomato leaf curl New Delhi virus. Transcriptome analysis revealed that 2927 genes were upregulated, and 2273 were downregulated in virus-infected pumpkin plants, compared to the gene expression in healthy pumpkin plants. Cluster analysis showed that the expression of genes related to RNA silencing and the salicylic acid resistance pathway was higher in virus-infected pumpkin plants than in healthy pumpkin plants. Furthermore, quantitative real-time PCR confirmed that the expression pattern of genes related to RNA silencing and the salicylic acid resistance pathway aligned with the transcriptome sequencing results. Our findings provide a reference for investigating the mechanism of mixed infections by these two viruses to aid in the prevention and control of viral diseases in pumpkins.