Currently, the safety and efficacy of Chinese materia medica have been questioned. Encountering that situation, this paper systematically elaborated on the cognitive process and basic connotation of the toxicity and efficacy of Chinese materia medica. A new thought and methodology of “multidimensional evaluation and integrative analysis of the toxicity and efficacy of TCM” was proposed. Taking Radix Aconiti Lateralis Praeparata as an example, the breeds, quality, pharmaceutical manufacture, medicinal properties, medicinal effects, and application of Radix Aconiti Lateralis Praeparata were used to evaluate the toxicity and efficacy systematically. Furthermore, the material basis, mechanism, and principle of effect-enhancing and toxicity-reducing of Radix Aconiti Lateralis Praeparata were integrated analyzed.