With the expansion of the aquaculture industry—in terms of scale and intensity—the single-minded pursuit of output has led to the deterioration of the aquaculture environment and frequent outbreaks of diseases, which has resulted in the diminished quality of aquatic products and safety of aquatic foods. The importance and urgency of realizing the concept of a healthy aquaculture industry is discussed herein, including the formation and development of this concept and corresponding key technologies. Suggestions and strategic measures for the operations and expansion of healthy aquaculture are put forward from perspectives based on science and technology, industry, policy and regulations.