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A crossover QCD phase transition in the early Universe, involving a formation scenario of stable strangeon nuggets is studied. The Polyakov-Nambu-Jona-Lasinio model is applied to calculate the thermodynamics of the QCD phase with u, d, s quarks, and the relativistic mean-field model describes the hadronic matter. The crossover phase transition from quarks to hadrons occurred at cosmic temperature of T~170 MeV, and those two phases are connected in a three-window model. Due to quark's non-perturbative coupling, quark clusters with net strangeness (i.e., strangeons) and then strangeon nuggets could form during the transition process. A distribution function of the nugget baryon number, A, is introduced to describe the nuggets' number density. All the strangeon nuggets with A>A_c are considered to be stable, where the critical number, A_c, is determined by both the weak and strong interactions. A non-relativistic equation of state is applied to calculate the thermodynamics of stable nuggets. The calculation shows that the thermodynamical contributions (pressure, entropy, etc.) of the stable strangeon nuggets are negligible. The resultant mass density of the strangeon nuggets survival from the early Universe is comparable to the dark matter, that indicates a possible explanation of the cold dark matter without introducing any exotic particles beyond the standard model.