Owing to the weak self-assembly ability of precursor components and the unadjustable limitation of micelle structures during assembly process, the synthesis of mesoporous colloidal nanospheres with sophisticated multimodal pore system remains a great challenge. Herein, we report a programmable shear-induced dynamic assembly approach to synthesize radially gradient-structured mesoporous carbon nanospheres with tunable core-shell architectures. Detailed mechanism studies reveal that the micelle structures in our system can be well adjusted by changing the shear force. More importantly, the synthetic process can be programmatically proceeded by setting up an on-demand stirring model, resulting in the intelligent assembly of multimodal mesostructures. The resultant mesoporous carbon nanospheres show small particle size, high surface area, abundant nitrogen species, and radially oriented open-porous structure and, as a result, deliver high capability and ultra-long cyclic life for sodium-ion storage. This facile programmable assembly approach would offer new opportunities in exploring sophisticated multimodal mesostructures for innovative applications. Multimodal porous structures are commonly found in living organisms and are of key importance to achieve optimal properties and performance. However, the progress in rational synthesis of nanomaterials with multimodal porous system remains unproductive. Herein, we demonstrate a programmed intelligent micelles assembly approach to synthesize a novel type of mesoporous carbon nanospheres with radially gradient pores and interesting core-shell architectures. In this synthesis, the micelle size can be precisely and dynamically controlled by manipulating the shear force through adjusting stirring rate; thus, the self-assembly process can be programmatically proceeded by setting up on-demand stirring modes. Such a simple yet effective method may open up new horizons to produce numerous delicate nanostructures with high level of functionalities for many practical applications, such as biosensor, nanomedicine, and energy storage. We have demonstrated a programmable shear-induced dynamic assembly approach to synthesize gradient-pore mesoporous carbon nanospheres with interesting core-shell architectures. The micelle structure in this synthetic system can be dynamically and programmatically tuned on demand by simply adjusting the shear force. The resultant gradient-pore mesoporous carbon nanospheres deliver excellent storage capability and ultra-long cycling stability for sodium-ion storage. This facile programmable assembly approach may offer new opportunities in exploring sophisticated multimodal mesostructures for various practical applications.