In practice, pesticides are usually applied simultaneously or one after another for crop protection, and this type of pesticide application often leads to a combined contamination of pesticide residues in the soil environment. A laboratory study was conducted to investigate the influence of chlorothalonil on chlorpyrifos degradation and its effects on soil bacterial, fungal, and actinomycete populations. Under the experimental conditions here, the half-lives of chlorpyrifos alone, and in combination with chlorothalonil, at the recommended and double dosages, were measured to be 3.24, 2.77, and 2.63 d, respectively. Chlorpyrifos degradation was not significantly altered by its combination with chlorothalonil. However, the inhibitory effect of chlorpyrifos on soil microorganisms was increased by its combination with chlorothalonil, and the increase was related to the levels of chlorothalonil added. Compared to those in the controls, the populations of bacteria, fungi, and actinomycetes were significantly reduced by 44.1%, 61.1%, and 72.8%, respectively, on the first day after treatment (DAT) by chlorpyrifos alone. With the addition of chlorothalonil, the inhibition was increased to 55.2%, 79.3%, and 85.8% at the recommended dosage, and 86.0%, 94.1%, and 90.8% at the double dosage, at one DAT, respectively. The results suggested that combined effects should be taken into account to assess the actual impacts of pesticide applications.