Environmental context Elemental selenium plays an important role in maintaining human health and the growth of plants and animals. We studied the availability of selenium in soils and agricultural crops in Guiyang City, China, and found that the soil is selenium-rich and the crops are selenium-enriched. These results can help to understand and improve the development of mountain agriculture and rural revitalisation. Rationale Selenium (Se) is a critical element for both maintaining human health and the growth of plants and animals. The content of Se in crops is primarily determined by its speciation in soil. Therefore, the investigation of soil Se and its speciation has become a key focus of current research. Methodology In this study, taking a typical seleniferous area in Guiyang City as the study area, we investigated selenium speciation in Se-rich soil and its distribution characteristics in both soil and crops using atomic fluorescence spectroscopy (AFS) and a five-step extraction processing methods. Moreover, we further explored the key factors that affect the distribution of Se in soil. Results The findings are summarised as follows: (1) the Se content in all investigated samples met the standards of selenium-rich soil (0.40 mg/kg). The Se content in the soil surrounding crop roots ranged from 0.96 to 4.29 mg/kg, with an average value of 2.18 mg/kg. (2) Soil Se primarily existed in organic, residual, and iron and manganese oxide-binding species. The organic, sulfide-binding, and elemental Se species were the major contributors, accounting for an average of 47.00%, while the content of water-soluble, exchangeable, and carbonate-binding Se species was significantly lower. (3) Almost all crops, regardless of their types, were found Se-enriched, accounting for approximately 89.47% of the total crops in the study area. The average Se content was 0.35, 0.12, and 0.026 mg/kg in tea, rice, and corn, respectively. Discussion Varying soil physical–chemical properties, such as the content of soil organic matter content and pH levels, etc. can impact the distribution of Se in soil differently. These findings can serve as a scientific foundation for the effective utilisation of selenium-rich land resources in Guiyang city. They can also support and facilitate the development of modern specialty and high-efficiency mountain agriculture, ultimately contributing to rural revitalisation and the national implementation of the Big Ecology Strategy.