The lack of Late Cretaceous stratum, as a longstanding problem, has been regarded in Kuqa Basin, due to a tectonic uplift. By studying the Late Cretaceous nannofossils founded recently in the upper member of the Bashijiqiuke Formation, marine upper Cretaceous and sedimentary environment in this basin are defined. On the basis of the Late Cretaceous ostracoda, charophytes founded in samples from drillholes, continental upper Cretaceous and sedimentary environment in this basin are fixed. Both analyses on sedimentary facies of the Bashijiqike Formation represented marine deposition and the Gucheng Formation represented continental deposition is made in this paper.