The trace elements and rare earth elements and the organic geochemical abundance of the Middle Permian carbonate and mudstone source rocks are analyzed systematically for the first time in the northern Xinjiang region, including the Junggar basin, the Turpan-Hami basin and the Ili basin. The results show that compared with the clarke of similar rocks, the contents of trace elements are either higher or lower. The light rare earth elements are relatively enriched and the content of heavy rare earth elements is relatively low. Besides, the Ce/Ce* ratio shows an obviously positive anomaly. They reflect that the sedimentary environments of the source rocks are mainly reducing environments. The geochemical analysis confirms that the content of trace elements has some effects on the distribution of the organisms in sedimentary water bodies. The abundance of some trace elements shows an obviously positive correlation with the content of organic matter. The study demonstrates that the sedimentary face zones of strongly reducing environmenst are batter sites for the deposition of primary organic matter, where the organic matter can be buried and preserved contemporaly, so that the source rocks are generally high in organic content, and vice versa.