Mechatronics system is the combination of mechanical system and control system. Based on the research of mechatronics system, the control kernel architecture based on embedded ARM and field bus is proposed, which takes mechanical system as the control object, takes sensors and drivers as control interface. To meet the need of flexible manufacturing and reconfigurable design, a reconfigurable technique based on field-programmable gate arrays (FPGAs) are applied, which has the potential for greater functionality and higher performance, but with smaller volume and lower power dissipation. Then, the hardware platform is applied into a typical embedded mechatronics system-CNC system. To solve the chaotic expansion in interfaces and the fallibility in operating, distributed structure and control based on PROFIBUS-DP is introduced into the system design. In the end, a machining centre based on the CNC system has proved that the mechatronics system meets the strict demand of function, reconfigurable and reliability.