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Mg-based porous materials, as potential bone tissue engineering scaffolds, are considered an attractive strategy for bone repair owing to favorable biodegradability, good biocompatibility and suitable mechanical properties. In this work, 3D-cubic interconnected porous Mg–xZn–0.3Ca (x = 0,3,6) scaffolds were prepared to obtain desirable pore structures with a mean porosity up to 73% and main pore size of 400–500 µm, which pore structures were close to the human cancellous bone. The structure–property relationships in the present scaffolds were analyzed by experiments and theoretical models of generalized method of cells (GMC). Mg–xZn–0.3Ca scaffolds exhibited good compression properties with a maximum above 5 MPa in yield strength and about 0.4 GPa in elastic modulus. This was attributed to not only the alloy strengthening but also the large minimum solid area. On the other hand, the scaffolds showed undesirable and relatively serious degradation behavior in Hank's solution, resulting from Zn addition in Mg-based scaffolds and the high surface area ratio in the pore structure. Therefore, surface modifications are worth studying for controlled degradation in the future. In conclusion, this research would explore a novel attempt to introduce 3D-cubic pore structure for Mg-based scaffolds, and provide new insights into the preparations of Mg-based scaffolds with good service performances for bone repair.