Abstract: The control factors of selenium content and migration rule in the parent rock-root soil-rice system in sedimentary rock areas (carbonate rock and shale) were studied to enrich the theory of selenium migration and transformation and further support the scientific utilization of selenium-rich land.The Se values of shale, corresponding soil and rice seed are 0.03~1.97 mg/kg, 0.27~2.38 mg/kg and 0.02~0.16 mg/kg, respectively, and carbonate rock, soil and rice seed show Se content of 0.02~0.12 mg/kg, 0.21~1.33 mg/kg and 0.02~0.12 mg/kg.The proportion of organic binding Se and residual Se in soil is up to 98%.The Se bioavailability of soil in shale area is 0.69%, which is lower than that in carbonate rock area (1.58%).The mineral and chemical compositions as well as content and modes of occurrence of Se in parent rocks play an important role in controlling physicochemical properties and Se content in soils.The content and bioavailability of Se in soil are predominantly controlled by soil pH and colloids.The strong adsorption of Se by organic matter and clay minerals is the main factor responsible for high content but low bioavailability of Se in soils.The decrease of pH results in the increase of Se adsorption by soil colloids and thus high Se content in soil.However, Se bioavailability shows a decrease trend with pH decreases.In summary, the soils in shale and carbonate rock areas show high content but low bioavailability of Se and consequently, low Se content in rice seed.Therefore, the total Se content in soils could not be regarded as the criterion for the exploration of Se-rich soil, and the soil properties and Se bioavailability should also be cautiously considered.