An integrated micro xy-stage is designed and fabricated for application in nanometer-scale operation and nanometric positioning precision. This device integrates the functions of both actuating and sensing in the same silicon ship and is mainly composed of a silicon-based xy-stage, electrostatics comb actuator and a displacement sensor. In this paper a robust control strategy based on single neuron adaptive PID control theory is developed for silicon-based xy-stage, considering electrical, mechanical, and stiffness models. Single neuron adaptive PID control enables compact realization of a robust controller tolerant of device characteristics variation, types of inherent instabilities, and improving dynamical characteristics. The experimental results verified that the controller is more suitable for the silicon integrated micro xy-stage, under which the settling time is less than 2.5ms and the repeatability error is better than ±24.9nm. In addition, the presented control scheme is simple to implement in practical application.