We describe a micromanipulation and pick-up system for preparing a micrometer-sized single particle for X-ray diffraction characterization. Combining a microgripper based on microelectromechanical systems, piezo-motor-driven linear stages, and a gamepad, the system provides precise and intuitive handling of the object. Single-crystal X-ray diffraction measurements of Sm-Fe-N permanent magnet were performed using this system. We also describe a method to distinguish crystallographically homogeneous particles found in powder-form samples.