In recent years, studies of traditional medicinal plants have gradually increased worldwide because the natural sources and variety of such plants allow them to complement modern pharmacological approaches. As computer technology has developed, in silico approaches such as virtual screening and network analysis have been widely utilized in efforts to elucidate the pharmacological basis of the functions of traditional medicinal plants. In the process of new drug discovery, the application of virtual screening and network pharmacology can enrich active compounds among the candidates and adequately indicate the mechanism of action of medicinal plants, reducing the cost and increasing the efficiency of the whole procedure. In this review, we first provide a detailed research routine for examining traditional medicinal plants by in silico techniques and elaborate on their theoretical principles. We also survey common databases, software programs and website tools that can be used for virtual screening and pharmacological network construction. Furthermore, we conclude with a simple example that illustrates the whole methodology, and we present perspectives on the development and application of this in silico methodology to reveal the pharmacological basis of the effects of traditional medicinal plants.