Although tumor models have revolutionized perspectives on cancer aetiology and treatment, current cell culture methods remain challenges in constructing organotypic tumor with in vivo‐like complexity, especially native characteristics, leading to unpredictable results for in vivo responses. Herein, we developed the bioorthogonal nanoengineering strategy (BONE) for building photothermal dynamic tumor spheroids. In this process, biosynthetic machinery incorporated bioorthogonal azide reporters into cell surface glycoconjugates, followed by reacting with multivalent click ligand (ClickRod) that was composed of hyaluronic acid‐functionalized gold nanorod carrying dibenzocyclooctyne moieties, resulting in rapid construction of tumor spheroids. We identified BONE could effectively assemble different cancer cells and immune cells together to construct heterogenous tumor spheroids. Particularly, ClickRod exhibited favourable photothermal activity, which precisely promoted cell activity and shaped physiological microenvironment, leading to formation of dynamic features of original tumor, such as heterogeneous cell population and pluripotency, different maturation levels, and physiological gradients. Importantly, BONE not only offered a promising platform for investigating tumorigenesis and therapeutic response, but improved establishment of subcutaneous xenograft model under mild photo‐stimulation, thereby significantly advancing cancer research. Therefore, we present the first bioorthogonal nanoengineering strategy for developing dynamic tumor models, which have the potential for bridging gaps between in vitro and in vivo research.This article is protected by copyright. All rights reserved