Chengdu-Chongqing region is located in Southwest China, a transition zone between the Se-poor belt in the middle and the Se-high belt in the southeast. The soil geochemical map shows that the Se content of topsoil in Xiushan area of Chongqing is (0.158 ~ 3.14)×10 ^-6, with an average of 0.457×10 ^-6. The soil selenium may come from the underlying black rock series: Niutetang carbonaceous shale of early Cambrian and phytoclastic and organic limestone of middle Permian, both of them might have been deposited among two Paleozoic transgressions. Nevertheless, selenium is deficient in soil of "red layer" in Bazhong and Nanchong, Sichuan. The Se values of topsoil are (0.084 ~ 0.510)×10 ^-6 and (0.033 ~ 0.349)×10 ^-6 respectively, with the average of 0.154×10 ^-6 and 0.140×10 ^-6. That might have been related to the transformation from late Triassic marine environment into Jurassic-Cretaceous continental sedimentary environment, causing selenium deficiency in continental lacustrine sandstone and siltstone.