A synthesis method for nanocomposite microspheres containing Ni nanoparticles via chemical surface modification has been developed, by which particle size and interparticle distance for embedded Ni nanoparticles can be systematically controlled. The process relies on introduction of carboxyl acid groups via hydrolysis of matrix polymer, incorporation of Ni ions via ion exchange reaction, hydrogen-induced reduction of doped Ni ions in the sphere followed by Ni nanoparticle-catalyzed decomposition of the surrounding polymer matrix. We demonstrate the formation of Ni nanoparticles in polymer microspheres and structural change of polymer matrix upon reaction by FT-IR, SEM, and cross-sectional TEM studies, and show that initial Ni ion loading determines final nanoparticle size ranging from 3 to 8 nm, which are homogeneously distributed in the whole of the microspheres. The heat-treatment in a hydrogen atmosphere at fixed temperature causes decomposition of the polymer matrix via catalytic reaction of Ni nanoparticles, resulting in a gradual increase in the volume fraction of the Ni phase in the spheres and thus decrease of the average interparticle distance. The process reported herein allows, therefore, one to independently control size and interparticle distance of Ni nanoparticles and is an effective methodology for preparing high-quality nanocomposites with a tailored microstructure which further allows control of functions.