Traditional Chinese medicine (TCM) follows the principle of formulae, in which the pharmacological activity of a single herb can be enhanced or potentiated by addition of other herbs. Nevertheless, the involved synergy mechanisms in formulae remain unknown. Here, a systems-based method is proposed and applied to three representative Chinese medicines in compound saffron formula (CSF): two animal spices (Moschus, Beaver Castoreum), and one herb Crocus sativus which exert synergistic effects for cardiovascular diseases (CVDs). From the formula, 42 ingredients and 66 corresponding targets are acquired based on the ADME evaluation and target fishing model. The network relationships between the compounds and targets are assembled with CVDs pathways to elucidate the synergistic therapeutic effects between the spices and the herbs. The results show that different compounds of the three medicines show similar curative activity in CVDs. Additionally, the active compounds from them shared CVDs-relevant targets (multiple compounds-one target), or functional diversity targets but with clinical relevance (multiple compounds-multiple targets-one disease). Moreover, the targets of them are largely enriched in the same CVDs pathways (multiple targets-one pathway). These results elucidate why animal spices and herbs can have pharmacologically synergistic effects on CVDs, which provides a new way for drug discovery.