We report on the unusual phenomenon of pattern formation in the thin film of Ni+C-60 mixture deposited on the MgO(100) substrate. Under certain deposition kinetics a periodic system of stripe domains was formed. The domains consist of sub-half-micrometer large droplets encompassed with a thin C-60-based rind with a possible polymeric structure. The stripes are embedded in the double-layer platform falling into the epitaxial Ni and amorphous-C (a-C) thin films. During co-deposition the C-60 molecules partly disintegrate and transform towards a-C. Due to the accumulation of a-C (with limited solubility in Ni) thermodynamic instability arises in the system and reaching a certain level, it triggers spontaneous partitioning (and self-organization) of the deposited material. As a principal mechanism of the pattern formation, a sequential drift and coordinate release of the thermodynamic instability is proposed.