Aim To design and construct the expression vector that can express the short interfering RNA(siRNA) against apolipoprotein M (ApoM)gene, screen the effective target sequence of siRNA and explore the function of ApoM. Methods The four siRNA against ApoM gene were transcript synthesized intracelluarly by expressed templates of plasmid vector pSilencerTM 2.1-U6, and the ApoM gene was inserted into the reporter gene in order to construct the recombinant plasmid vector plucF-ApoM. The recombinant plasmid and siRNA producing plasmid were cotransfected into 293T cells and screened out the effective siRNA that inhibiting the expression of luciferase, siRNA was transfected into L-02, the expression of ApoM mRNA was detected by reverse transcription polymerase chain reaction (RT-PCR) to further identify the inhibiting function of siRNA on ApoM expression, enzyme linked immunosorbent assay (ELISA) method was used to detect the effect of effective siRNA on synthesis and secretion of apolipoprotein A_Ⅰ (ApoA_Ⅰ), apolipoprotein B (ApoB), apolipoprotein E (ApoE). Results Two siRNA of the four synthesized siRNA displayed inhibitory effects on the lucifermase expression with the inhibitory rate being 86% and 91% respectively, the expression of ApoM mRNA was specially inhibited, effective siRNA could inhibit synthesis and secretion of ApoA_Ⅰ effectively (p<0.05), while there was no change in ApoB and ApoE secretion (p>0.05). Conclusion Effective siRNA plasmids against ApoM gene were constructed and screened out successfully which created a favourable condition for exploring the mechanisms of coronary heart disease.