The invention relates to the field of biotechnology, and provides improved identification for target RNA sequences bound to RNA-binding protein in cells. Through UV crosslinking-immunopricipitation, target RNA of RNA-binding protein is obtained, micrococcal nuclease is adopted for carrying out incomplete enzymolysis on the target RNA after ultraviolet crosslinking, after enzymolysis, a chelating agent capable of removing Ca<2+> is adopted for inactivating the enzyme, the 3' terminal of the target RNA obtained through the method is phosphorylated, the phosphorylated 3' terminal is ligated witha 3' RNA linker, then, the ligation product is phosphorylated, the phosphorylated ligation product is separated, the separated phosphorylated ligation product is recycled, then the 3' terminal is ligated with a 5' RNA linker, RT-PCR amplification is carried out, so that a cDNA library corresponding to the target RNA is obtained. With the technical scheme provided by the invention, the experiment flow is simplified, the step of isotope labelling is eliminated, due to the adding of an IgG antibody negative control sample, the influences of non-specific binding and background on the experimentalresult are eliminated, and the data result with the quality equal to that of Clip-seq is obtained.