As a key alloying element in magnesium (Mg) alloys, calcium (Ca) effectively enhances their oxidation resistance, high-temperature strength, and castability. However, experimentally determining the regulatory mechanism of Ca on the fluidity of Mg alloy melts remains challenging due to the high volatility and oxidation tendency of the alloy melts. To address this, molecular dynamics simulations are employed to systematically calculate the structural parameters (pair distribution function, coordination number, Voronoi index, and Honeycutt–Anderson index) and viscosity of Mg–Ca alloy melts across a Ca content range of 0.1–10 wt% (covering low concentrations to near the eutectic point of 10.5 wt%). At low Ca concentrations, the degree of structural order in the melt exhibits oscillatory changes with increasing Ca content (< 4 wt%), accompanied by significant structural fluctuations. In contrast, the structural order increases slightly with Ca content at high Ca concentrations (> 4 wt%), leading to enhanced structural stability. Throughout the entire Ca concentration range, ICO-type bonded pairs remain predominant, underscoring their critical role in maintaining the short-range ordered structure. As the Ca content increases, the atomic diffusion capability decreases, while the melt viscosity shows an overall increasing trend, with values calculated via both equilibrium molecular dynamics and nonequilibrium molecular dynamics methods confirming this trend. This study provides a microscopic theoretical basis for elucidating the regulatory mechanism of Ca on the fluidity of Mg–Ca alloy melts by establishing a quantitative correlation between Ca content, melt structure, and viscosity.