Density functional theory (DFT) was utilized to simulate the reactions occurred in the mixture solution of cysteine and Hg(II) ions with the ratio < 2. Simulation result shows that Hg ions will coordinate to cysteine by the thiol groups with the form of S–Hg2 and S–Hg3, and moreover, the content of free Hg ions can only be reduced by these two forms. OH− plays an important role in the growth of β-HgS, because its nucleophilic substitution reaction supplies plenty of Hg–S–Hg radicals, which will be adsorbed onto the surface of liquid mercury ball and form the precursor of β-HgS(111) plane. Three valent bonds adsorption of Hg–S–Hg radicals onto the surface of Hg ball has more adsorption energy (−32.768 kcal mol−1) than that of two valent bond adsorption (−20.882 kcal mol−1). Hg balls will stop growing after completely covered with Hg–S–Hg radicals and their size will be limited. The growth direction of β-HgS is parallel to the “repelling” force, that is [111] direction in β-HgS lattice. The calculated results are in good agreement with the experimental observations, demonstrating that the DFT method can be taken as a very useful tool to interpret the solution reactions that cannot be solved by conventional methods.