The hexamethyldisilazane-assisted synthesis of organic-free copper sulfide microflowers is described herein. The synthetic method was developed in such a way as not to leave any trace of organic material in the copper sulfide nanoparticles after purification. The flowers were constructed by the self-assembly of nanoflakes. Copper sulfide was formed via an S–N polymeric intermediate, which drives the formation of copper sulfide by elmination of trimethylsilyl chloride as a key product. A reaction mechanism has been proposed based on the results of time-dependent NMR studies. The self-assembly and stability of the microflowers are explained on the basis of analytical data.