Environmental risk communication is the key point of environmental governance. Due to the limitations of the “persuasion knowledge model” led by officials and experts, the construction of a “mutual way communication path” with Chinese local characteristics has received attention from both academic and practical circles. What is the role of Non-Governmental Organizations as spokespeople and evangelists for the public in the field of risk communication? Can they break out of their passive role as “information receivers” and reverse the direction of communication? This paper takes waste incineration risk controversy as an example, and uses content analysis, text analysis, and ethnography to observe nine organizations and their Wechat official accounts, condensing the logic of “knowledge-based” risk communication. In other words, Non-Governmental Organizations are driven by the goal of “knowledge negotiated risk communication”, the pressure of “double knowledge shortage” and the positive incentive of “knowledge adoption”. In the concept of “scientific philanthropy”, relying on the organizational guarantee of “knowledge community”, Non-Governmental Organizations use five techniques of knowledge picking, linking, condensing, visualizing and fixing to integrate authoritative, expert, practical and experiential knowledge, and present four issues of risk warning topics including warning, tracing, mitigation and reflection. On one hand, this study will help to expand the theory of risk communication, promote its refinement and localization. On the other hand, it provides a perspective on the action space of Non-Governmental Organizations in the process of modernizing China’s environmental governance system and capacity, and helps to understand the future trend of the relationship between government and society.