Amorphous transition metal oxides exhibit exotic transport and magnetic properties, while the absence of periodic structure has long been a major obstacle for the understanding of their electronic structure and exchange interaction. In this paper, we have formulated a theoretical approach, which combines the melt-quench approach and the spin dynamic Monte-Carlo simulations, and based on it, we explored amorphous Co0.5Zn0.5O1−y ternary transition metal oxides. Our theoretical results reveal that the microstructure, the magnetic properties, and the exchange interactions of Co0.5Zn0.5O1−y are strongly determined by the oxygen stoichiometry. In the oxygen-deficient sample (y > 0), we have observed the long-range ferromagnetic spin ordering which is associated with the non-stoichiometric cobalt-rich region rather than metallic clusters. On the other hand, the microstructure of stoichiometric sample takes the form of continuous random networks, and no long-range ferromagnetism has been observed in it. Magnetization characterization of experimental synthesized Co0.61Zn0.39O1−y films verifies the relation between the spin ordering and the oxygen stoichiometry. Furthermore, the temperature dependence of electrical transport shows a typical feature of semiconductors, in agreement with our theoretical results.