Viruses are an important component of the food web, and have vital functions in the ecosystem. Viruses can affect the mortality, community structure and evolution of their hosts and nutrient cycling. However, we know little about community composition and functional characteristics of viruses in soil, due to technical challenges. To initially explore the characteristics of soil virome under different land-use types, cotton soil and desert soil were collected in Xinjiang. Twenty and fifteen viral families were identified from cotton soil and desert soil, respectively, and ssDNA viruses were predominant in both two samples, with Microviridae being the most abundant family. Caulimoviridae, Retroviridae, Nudiviridae, Polydnaviridae, Baculoviridae, and Ascoviridae were only detected in cotton soil, most of which belonged to plant and insect viruses. This study speculates that the difference of human activities, soil physical and chemical properties, plants and animals associated with different land-use types might affect viral communities. A total of 1824 viral contigs were identified by Virsorter and mainly annotated to the family Microviridae. Major functions of two viromes were similar by comparison with the SEED database, and at SEED subsystem level 2 annotation, "Phage capsid proteins" and "Phage packaging machinery" accounted for the highest proportion. This study can provide data support for further exploration of soil virus ecological function and soil food web.