The Yangtze estuary is located in the most economically developed regions of China. It’s the golden waterway of the Yangtze River. With the rapid development of port throughput and economy, the shortage of land resources promoted wharf dredging and mining industry. Pursuing the maximum profit, small engineering ships carried out illegal operation such as throwing mud and sand from time to time, which destroyed the normal competition order and damaged the environment and channel conditions. So, it’s urgent for the government to strengthen management and curb the spread of illegal behaviors. Based on several years of practice, this paper summarizes the way of improving law enforcement supervision of small engineering ships in the Yangtze River estuary, which can be used for scholars and government departments to make better decisions.