Abstract Understanding how intrinsic defects impact magnesium (Mg) crystals mechanics is of prime importance for engineering applications. In this work, the mechanical performance of Mg crystals with cracks at the nanoscale was studied using molecular dynamics method. Influence of the nano-crack type and size on the deformation behavior of Mg crystals was analyzed in details. The obtained results show that the mechanical properties of Mg crystals decrease with the increase of the nano-crack length (perpendicular to the tensile direction). However, the yield stress of Mg crystals is enhanced by increasing the nano-crack width (parallel to the tensile direction) while the nano-crack length remains unchanged. The effect of temperature on Young’s modulus of Mg crystals is weak along z -axis, while Young’s modulus along y -axis is clearly temperature-dependent. The yield stress of Mg crystals decreases with increasing temperature. The appearance of twins is the main deformation mechanism in Mg crystal along z -axis while the deformation begins with the formation of a prismatic slip along y -axis. The results obtained in this work would provide useful information for further mechanical properties regulation of Mg crystals.