Physalis Calyx seu Fructus (PCF) is a herb widely used in China for its function of clearing heat and detoxifying, benefitting the pharynx and reducing phlegm, both in health care and in tea drinking. However, the quality of its fruit and calyx is uneven and the storage period is short. Therefore, it is crucial to develop other parts of PCF with longer storage periods and obvious medicinal effects. Firstly, high-performance liquid chromatography was used to develop the fingerprint of different parts of PCF, and various chemometric analyses were conducted to screen out chemical markers. The calyxes of PCF were found to cluster together, distinct from the fruits, roots, stems and leaves. The active components of PCF were concentrated in the persistent calyxes, and flavonoids were mainly found in the persistent calyxes and leaves. Secondly, the extraction of persistent calyxes showed the strongest scavenging ability of DPPH and ABTS. Finally, the important chemical markers were verified by network pharmacological analysis and molecular docking. It provides a reference for the clinical application of PCF, and the obtained chemical markers offer a scientific basis for quality evaluation.