Toddalia asiatica (Linn) Lam ( T. asiatica) as a traditional Miao medicine was investigated to find rational alternative medicinal parts for T. asiatica root bark and its antitumor chemical constituents by quantitative pharmacognostic microscopy, high performance liquid chromatography (HPLC) fingerprint and multivariate statistical analysis. A bivariate correlation analysis method based on microscopic characteristics and content of chemical constituents was established for the first time, there were some regular discoveries between powder microscopic characteristics and common chromatographic peaks of T. asiatica through quantitative pharmacognostic microscopy, cork cells, calcium oxalate square crystal, brown clump, starch granule and phloem fiber, as powder microscopic characteristics may be placed where the main chemical constitutes were enriched. Scores plot of principal component analysis (PCA) and dendrogram of hierarchical clustering analysis (HCA) showed that 18 T. asiatica samples were distinguished correctly, clustered clearly into two main groups as follows: S01∼S03 (root bark) and S07∼S09 (stem bark) in cluster 1, S04∼S06 and S10∼S18 in cluster 2. Nineteen common peaks were obtained in HPLC fingerprint of T. asiatica, loadings plot of PCA indicated seven compounds played important roles in different part of samples (P10 > P08 > P07 > P14 > P16 > P17 > P19), peaks 04, 06, 07, 08, 10 were identified as hesperidin, 4-methoxycinnamic acid, toddalolactone, isopimpinlline and pimpinellin. MTT assay was used to determine the inhibitory activity of different medicinal parts of T. asiatica on human breast cancer MCF-7 cells, all parts of T. asiatica had different inhibitory effects on MCF-7 cell lines, root and stem barks of T. asiatica showed the best inhibitory activity. The relationship between chemical constituents and the inhibitions on MCF-7 cell had been established, significant antitumor constituents of T. asiatica were identified by correlation analysis, the order of the antitumor effect of the main compounds was P07 (toddalolactone) > P16 > P06 (4-methoxycinnamic acid), P11 > P18 > P10 (pimpinellin) > P08 (isopimpinellin) > P01 > P19 > P14 > P04 (hesperidin) > P17, which were antitumor chemical constituents of T. asiatica root bark. T. asiatica stem bark was the most rational alternative medicinal part for T. asiatica root bark.