with nanoparticles (NPs) has emerged as a promising strategy for maximizing the effectiveness of combination therapies by simultaneously regulating various pathways. [2] Despite some advancements, different types of pharmaceuticals have significantly diverse physicochemical properties, and thus it remains a major challenge to achieving efficient co-loading of different pharmaceuticals at a defined ratio in a single nanoparticle. Additionally, characterizations of their pharmacological and physicochemical properties are typically conducted using physical, chemical, and biological analyses. [3] However, without molecular or atomic-level information, it is difficult to design, evaluate, and optimize a co-delivery nanoformulation to achieve better and safer therapeutic/prognostic effects. Simulations with an increased computational capacity have been developed to accurately describe atomic or molecular interactions in nanomedicines, enabling bottomup approaches of designing nanoparticles for combination therapy. [4] So far, there has been no report of the de novo design Combination therapy is a promising approach for effective treatment of tumors through synergistically regulating pathways. However, the synergistic effect is limited, likely by uncontrolled co-delivery of different therapeutic payloads in a single nanoparticle. Herein, a combination nanotherapeutic is developed by using two amphiphilic conjugates, hyperbranched poly(ethylene glycol)-pyropheophorbide-a (Ppa) (HP-P) and hyperbranched poly(ethylene glycol)-doxorubicin (DOX) (HP-D) to construct co-assembly nanoparticles (HP-PD NPs) for controllably co-loading and co-delivering Ppa and DOX. In vitro and in vivo antitumor studies confirm the synergistic effect of photodynamic therapy and chemotherapy from HP-PD NPs. Metabolic variations reveal that tumor suppression is associated with disruption of metabolic homeostasis, leading to reduced protein translation. This study uncovers the manipulation of metabolic changes in tumor cells through disruption of cellular homeostasis using HP-PD NPs and provides a new insight into the rational design of synergistic nanotherapeutics for combination therapy.