To analyze the enrichment characteristics and correlation of Se and heavy metals in soil-blueberry fruit systems in different geological background areas of Guizhou Province, 86 soil samples and 58 blueberry fruit samples were collected from blueberry planting areas in the Majiang, Ziyun, and Huangping counties of Guizhou Province. The contents of Se and 9 other heavy metals in soil and blueberry fruit were determined using an inductively coupled plasma mass spectrometer (ICP-MS) and inductively coupled plasma emission spectrometer (ICP-AES). The results showed that the Se contents of the soils in the dolomite and limestone distribution areas are higher than the background values of topsoil in Guizhou, and both met the Se-rich soil standard. The Se content of the soil in the study areas exhibits the characteristics of limestone area>dolomite area>sandstone area, indicating that the geological background controls the Se content of the soil. In dolomite soil, Se is negatively correlated with As, Cu, Hg, Ni, Pb, and Zn, while in limestone soil, Se is positively correlated with As, Cr, Ni, and Zn. In dolomite and limestone areas, the Se in soil is negatively correlated with Hg and Pb in blueberry fruit. There is no significant correlation in the sandstone area. The blueberries in each growing area have a high enrichment capacity for Se and have all reached the selenium-rich blueberry standard, which has the potential for development into selenium-rich blueberry agriculture.