Crystalline-to-amorphous transitions induced by chemical modulation have been attracting great research interests and an in-depth understanding of such transitions is always demanding. Here we design the Nb-Ti-Zr-(Si) alloy systems employing the empirical criteria and the related phase diagrams for enhancing mechanical properties accompanied by Si-induced microstructure evolutions. (NbTiZr)100-xSix (x = 0, 3.0, 10.2, 22.2, and 25.0 at.%) refractory medium-entropy alloy (RMEA) coatings are synthesized by magnetron co-sputtering. With increasing Si content, the pristine body-centered cubic (bcc) single phase transforms into a nanocomposite structure consisting of bcc nanocrystals embedded in an amorphous matrix and eventually into an entirely amorphous structure. This is well rationalized with a thermodynamic database of the Nb-Ti-Zr-Si system constructed using the CALPHAD (CALculation of PHAse Diagrams) approach, which suggests the bcc structure to be thermodynamically stable at low Si contents and the formation of amorphous RMEA to be preferred at higher Si contents. The superior mechanical property of the amorphous (NbTiZr)75.0Si25.0 (at.%) coating compared to the Si-free counterpart is achieved, i.e., the hardness (H) increases by 115% and the elastic modulus (E) increases by 70%. The Si-induced crystalline-to-amorphous transition in RMEA which leads to a consistently impressive strengthening effect was rarely found in other alloys or coatings.