MpSDockZn is a zinc metalloprotein-specific molecular docking program, which employs NSGA II, a multi-objective optimization algorithm, to search the binding poses of a ligand to its metalloprotein receptor. Meanwhile, we designed a zinc metalloprotein-specific force field-based scoring function based on the recently reported zinc metalloprotein-specific non-bonded pairwise force field SLEF and developed a new zinc metalloprotein-specific knowledge-based scoring function based on the inverse Boltzmann law, nonlinear constrained optimization, and a designed dynamic sampling and iteration optimization strategy. These zinc metalloprotein-specific atom-pair potentials can reasonably and quantitatively describe the characteristics of different interactions between different atom-pairs, providing insights into the functions of these atom-pair potentials and highlighting important atom-pair interactions, such as coordination bonds, hydrogen bonds, and electrostatic interactions, thereby enhancing the ability to identify true-positive molecules and avoid the false-positive results. MpSDockZn is available at this site.