The nuclear suppression of heavy quarkonium production at low transverse momentum in pA collisions in high energy scatterings is investigated in the small-x factorization formalism. A universal suppression is found in the large Nc limit between the two formalisms to describe the heavy quarkonium production: the non-relativistic QCD (NRQCD) and the color-evaporation model (CEM). This provides an important probe to the saturation momentum at small-x in big nucleus. We also comment on the phenomenological applications of our results.