Industrial structure affects the degree of environmental changes, and different industrial structures are characterized with different environmental conditions. The structure of the industrial economy, upon which China’s economic growth bases, has caused great pollution to China’s ecological environment. Therefore, the protection of ecological environmental brooks no delay. Based on the perspective of environmental governance, this article constructs a multi-objective optimization model of the industrial structure, and with the panel data, it analyzes the optimal structure of the industrial structure of Pearl River Delta, provides a theoretical basis for the environmental governance and industrial structure optimization of the Pearl River Delta, and proposes policy recommendations to promote environmental pollution control and industrial structure optimization in Pearl River Delta.