The vector psi-CHECK2 is widely used to validate the interactions of microRNA with mRNA. Typical primers for recombinant psi-CHECK2 are usually designed as protective bases at 5 end of DNA (5 prime) followed by enzyme restriction sites with partial target sequences at 3 end of DNA (3 prime). However, the recombinant efficiency of psi-CHECK2 is usually not high enough to fulfill our molecular experiments. Here, we demonstrated that using ∼15 bases of each dangling ends of linearized psi-CHECK2 instead of traditional protective bases could easily improve the recombinant efficiency of psi-CHECK2. In this study, the T4 ligation products of linearized psi-CHECK2 and digested PCR products were transformed into DH5α. The results showed that compared with the conventional primers, our improved primers have better performance in the number of bacterial colonies, the positive rate of PCR amplifications of bacterial solutions of randomly selected colonies, and the recombinant efficiency confirmed by Sanger sequencing. We also co-transformed the linearized psi-CHECK2 and digested PCR products without T4 ligase treatment to estimate the effects of endogenous homologous recombination of DH5α. Indeed, endogenous homologous recombination could promote the recombinant efficiency of psi-CHECK2 but was significantly lower than that of our method (combination of improved primers and T4 ligase treatment). This method may be an alternative to the constructions of other recombinant vectors.