Selenium (Se) is an essential trace element for humans and animals. In China, intensive agricultural inputs in greenhouse vegetable production (GVP) have resulted in great changes in Se concentration and bioavailability in soil, which have great influences on Se flux to living organisms through food chains. It is crucial to understand the factors on Se concentration and bioavailability in greenhouse soil. Thus, we chose the east bank of the Dianchi Lake, a typical GVP area covering 177 km² in Southwest China, as the study area to quantify source contributions to soil Se and estimate relative importance of influence factors on its bioavailability in GVP with a receptor model (absolute principal component scores-multiple linear regression, APCS-MLR) after principal component analysis (PCA). According to the enrichment factor (EF), total Se in greenhouse soil was accumulated at a minor level (1 < EF < 3) by long-term and intensive fertilization. Source contributions to total Se decreased in the sequence of parent materials > fertilization > atmospheric deposition. It suggested that fertilization, especially manure, might be an important way to increase total Se in greenhouse soils in Se-deficient areas. The bioavailability of Se was affected by several factors, among of which total Se was the foremost one. In comparison with organic matter and clay, Fe/Al oxides exerted more controls on Se bioavailability, which was dependent on pH. Increasing Olsen P was helpful in improving soil Se bioavailability in greenhouse. More attention should be paid to soil physicochemical characteristics when Se-containing fertilizers are applied to increase Se levels in greenhouse vegetables.