Several effective constituents, such as vanillin, ferulic acid, senkyunolide I, senkyunolide H, coniferyl ferulate, Z-ligustilide, butylphthalide, senkyunolide A, and levistilide A, are unstable and possess mutual transformation relationships in Chuanxiong Rhizoma (CR). Traditional Chinese medicine mainly involves decoction, and the content of effective constituents and antiplatelet aggregation bioactivity (AAB) in CR may vary with different decoction time (10 min, 20 min, 30 min, 40 min, 50 min, and 60 min). Here, we showed that coniferyl ferulate and levistilide A were detected in CR material, but not in the decoction. The effective components possessed transformation and degradation in CR decoction of different times. The effective components and the strength of AAB at 10 and 20 minutes were the strongest, followed by 30–50 minutes, and 60 minutes were the weakest by analysis of SIMCA-PLS in CR decoction of different times. In the Pearson correlation analysis, there were correlations (P < 0.05) between effective components, which were ferulic acid and senkyunolide I (coefficient was 0.976), ferulic acid and senkyunolide H (coefficient was 0.972), senkyunolide I and senkyunolide H (coefficient was 0.982), senkyunolide A and butylphthalide (coefficient was 0.974), senkyunolide A and Z-ligustilide (coefficient was 0.947), and butylphthalide and Z-ligustilide (coefficient was 0.993). Effective components (ferulic acid, senkyunolide I, and senkyunolide H) and AAB were correlated and the Pearson correlation coefficients were respectively 0.965, 0.973, and 0.999. In the stepwise regression analysis, senkyunolide H and senkyunolide I were correlated with AAB (P < 0.05). Senkyunolide H (H) was positively correlated with AAB, senkyunolide I (I) was negatively correlated with AAB, and its expression was AAB = 1.187 ∗ H − 0.199 ∗ I − 0.422. These findings indicate that there are some correlations between effective components and AAB in CR.