Calcium silicate-based cement has been widely used for endodontic repair. However, it has a long setting time and needs to shorten setting time. This study investigated the effects of magnesium (Mg) ion on the setting reaction, mechanical properties, and biological properties of calcium silicate cement (CSC). Sol-gel route was used to synthesize Mg ion-doped calcium silicate cement. Synthesized cement was formulated with the addition of different contents of Mg ion, according to 0, 1, 3, 5 mol% of Mg ion-doped calcium silicate. The synthesized cements were characterized with X-ray diffraction (XRD), Fourier transformed infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM). We also evaluated the physicochemical and biological properties of cement, such as the setting time, compressive strength, micro-hardness, simulated body fluid (SBF) immersion, cytotoxicity, and cell differentiation tests. As a result, the Mg ion improves the hydration properties of calcium silicate cement, and the setting time is reduced by increasing the amounts of Mg ion. However, the mechanical properties deteriorated with increasing Mg ion, and 1 and 3 mol% Mg-doped calcium silicate had appropriate mechanical properties. Also, the results of biological properties such as cytotoxicity, ALP activity, and ARS staining improved with Mg ion. Consequently, the optimal condition is 3 mol% of Mg ion-doped calcium silicate (3%Mg-CSC).