To accommodate the trend toward mass customization launched by intelligent manufacturing, the paper proposes the adoption of model-integrated computing (MIC) paradigm in the motion control system development process for enhancing flexibility and robustness. Hierarchical structural and behavioral diversities in motion control system are considered during the implementation of MIC paradigm. For design-phase implementation, a motion-control-domain-specific modeling language is developed, and formal semantics are integrated. With regard to execution-phase implementation, a real-time runtime framework compliant with the IEC 61499 standard is proposed. Extensions of function block chain and priority-based event propagation are proposed. Dynamically extendable FB types library for motion control domain is constructed. A prototype three-axis motion control system is modeled using the proposed modelling language and is then deployed to the implemented framework to prove the feasibility of the adoption of the MIC paradigm in motion control domain.