Combination therapy using effective drug molecules and functional genes such as small interfering RNA (siRNA) has been suggested as a powerful strategy against multiple drug resistance. Here, we present a protocol for preparing a delivery system by developing dynamic covalent macrocycles using a dithiol monomer to co-deliver doxorubicin and siRNA. We describe steps for preparing the dithiol monomer, followed by co-delivery to form nanoparticles. We then detail procedures for cell uptake and assessing enhanced anti-cancer efficacy in vitro. For complete details on the use and execution of this protocol, please refer to Lyu et al.