With the rapid progress of nanotechnology, the development of multifunctional nanobiomaterials (NBMs) has brought about innovative strategies and improvements in tumor nanotherapy, particularly in achieving precise control over the therapeutic process for higher therapeutic efficacy while minimizing side effects. Considering the heterogeneous nature of the tumor microenvironment, NBMs need to be carefully regulated in terms of timing, location, and dosage. This gives rise to the concept of “programming nanobiomaterials (PNBMs)” to deliver the appropriate dose of drugs at the optimal time and site in response to endogenous or exogenous stimuli, thereby facilitating accurate tumor clearance. The objective of this article is to summarize current advances and applications of PNBMs in tumor nanotherapy. Additionally, it aims to discuss the utilization of PNBMs in tumor precision therapy in terms of component programming, size programming, hydrophilicity programming, cascade response programming, logic gate control programming, and multifactor response programming. Furthermore, we prospect the PNBMs fusion design, matching complicated microenvironments, degradability and safety, and clinical application potential, all of which will serve as a reference for the design and development of novel and efficient PNBMs in cancer nanotherapy.