Shanghai Port has been the world’s largest one in terms of container throughput for many years. Meanwhile, its capacity hits a bottleneck currently due to complex waterways, congested traffic flows, variable meteorological conditions, etc. In order to further increase the container throughput capacity, the Yangtze River Estuary Deep-water Channel, which serves as a vital route leading to the Shanghai Port, is focused on. Especially, risk analysis of container ships navigating in the channel in severe restricted visibility is conducted. The FMEA (Failure Mode and Effects Analysis) method is adopted to evaluate the risk. Based on the method, potential hazardous events that may occur in different sections of the waterway are obtained, and frequency index levels and severity index values are determined to construct a risk matrix. Subsequently, quantitative evaluations were carried out based on this risk matrix for dangerous events that could arise during container ship navigation within the Yangtze River Estuary Deep-water Channel in severe restricted visibility. Following the evaluation process, corresponding risk values and their respective grades in the risk matrix under different visibility conditions are obtained. Then, dangerous events occurring within the ALARP (As Low as Reasonably Practicable) area within 0–200 meters visibility range are analyzed specially, and measures aimed at reducing its frequency and mitigating its consequence are provided correspondingly. After a reevaluation, the risk events in the ALARP area are successfully lowered into the low-risk zone. This study has certain guiding significance for improving the container throughput of Shanghai Port and promoting the high-quality development of Shanghai International Shipping Center.