Objective To make a comparison between the antitumor effect and the chemical constituents of Huanglian Jiedu decoction (HLJDT) and that of serum containing HLJDT. Method Based on the established chromatographic fingerprint of HLJDT, analysis and comparison were made between the HPLC fingerprints of rat serum samples obtained after orally taking HLJDT and those of control rat serum samples. The different effects on NCI-H446 and Bel-74024 cancer cells from human were investigated in vitro using HLJDT and its serum. The inhibitory effects of HLJDT and its serum were observed by MTT assay. Result Ten compounds of HLJDT and some metabolites were detected after oral administration of HLJDT, and however some main compounds of HLJDT were not detected in serum. Both HLJDT and its serum in different dosage groups could inhibit the proliferation of NCI-H446 and Bel-7402 cancer cells from human in a dose-dependent manner, but inhibitory grade was different in the two cancer cell lines. HLJDT had more inhibitory effect on Bel-7402 than on NCI-H446, on the other hand serum containing HLJDT had the same inhibitory effect on Bel-7402 and NCI-H446. Conclusion The reason for inhibitory grade change was that the proportion of concentration of many compounds in serum containing HLJDT was different to that in HLJDT, which should be subject to thorough investigation so as to illuminate the pharmacology and active mechanism of HLJDT.