Pulp capping agents are effective materials which can preserve dental pulp and treat caries in different ways. It is urgently demanded to establish a guidance to select the appropriate pulp capping agents according to the conditions of pulp and cary requirements. In this work, morphology, composition, physical, and chemical properties of three commonly used clinical pulp capping agents, namely dental zinc oxide eugenol cement (ZnO), self-curing calcium hydroxide (Dycal), and light-curing calcium hydroxide (Calcimol), were studied. Their antibacterial, cytocompatibility and blood compatibility were evaluated. The results showed that ZnO was hydrophobic and its effective component, crystallized ZnO, could consistently release zinc ions, giving its alkaline environment to inhibit bacteria. Structure, morphology and components in Dycal were similar to those in Calcimol. However, its surface was more hydrophobic and its release amount of calcium ions was larger than that of Calcimol. It formed an alkaline micro-environment, thereby possessed good antibacterial ability and biocompatibility. Meanwhile, Calcimol was hydrophilic and convenient to operate, and released less metal ions. Due to its safe composition, Calciomol exhibited excellent biocompatibility but slightly weaker antibacterial property. Our results suggested that these comparative results might be a useful clinical guidance for selecting appropriate pulp capping agents according to the degree of caries and the health status of dental pulp to treat the caries.