The separation section of the methanol-to-olefin (MTO) process is energy-intensive, and the optimization and heat integration can enhance energy efficiency and reduce costs. A bi-level optimization model framework is proposed to optimize the separation process and simultaneously integrate the heat exchanger network (HEN). The upper level employs a data-driven BP neural network proxy model instead of the mechanism model for the separation process, while the lower level adopts a stage-wise superstructure for the HEN without stream splits. The interaction between the two systems is realized effectively through information exchange. A bi-level particle swarm algorithm is employed to optimize complex problems and determine the optimal operational parameters for the distillation system and HEN. Compared with the typical sequential synthesis method, the optimization by the proposed approach reduces the total annual cost by 1.4293×106 USD/y, accounting for 4.76%.