The flood of chemical substances in the environment result in the complexity of chemical mixtures, and one of the reasons for complexity is that their individual chemicals bind to different binding sites on different (or same) target proteins within the organism. A general approaches therefore are proposed in this study to predict the toxicity of chemical mixtures with different binding sites by using molecular docking-based binding energy (Ebinding). Aldehydes and cyanogenic toxicants were selected as the example of chemical mixtures with same binding site. Triazines and urea herbicide were selected as the example of chemical mixtures with different binding sites but on same target protein. Sulfonamides and trimethoprim toxicants were selected as the example of chemical mixtures with different target proteins. Although these chemical mixtures bind to their binding sites by different ways, there is a general relationship between their binary mixture toxicity (EC50M) and their corresponding Ebinding of individual chemicals and logKow(mix). By using the Ebinding to describe how the individual chemicals work in the different binding sites, the approach may provide a general and simply model to predict mixture toxicity to microorganism.