The identification of hazardous wastes serves an important technical basis and key step for recognizing the hazardous characteristics of industrial wastes. Hazardous wastes appraisal is a specialized activity aimed at determining the nature of waste in cases of environmental pollution involving waste and providing appraisal opinions. As one of the standards for the identification of hazardous wastes, the Identification Standards for Hazardous Wastes-Identification for Toxic Substance Content (GB 5085.6-2007) plays a vital role in identifying industrial wastes and appraising case-related wastes. By analyzing 50 identification reports and typical cases, this paper comprehensively reveals the issues existing in the practices of identifying toxic substances, particularly those composed of inorganic toxic components, in terms of detection methods, conversion methods, and result judgment. Furthermore, this paper analyzes the deviation between the implementation of the standard and the “in dubio pro reo” principle in practice, and proposes countermeasures to promote the development of a more comprehensive forensic system for hazardous wastes identification.