In the construction of water conveyance tunnels with the shield method, accidents have occurred from time to time, such as collapses and explosions, and it is of practical significance to explore the cause mechanism of the accident. However, previous research has not considered the effects of dependence between risks on the risk spread. In response, we propose a method based on the Natural Killing Model (the N-K Model) and complex network theory to analyze the cause of shield construction accidents in water conveyance tunnels. By deeply exploring the transmission mechanism and action intensity between system risks, this method can scientifically clarify the accident cause mechanism and provide support for engineering construction safety management. The method constructs a risk index system. Secondly, we introduce the N-K model to reveal the risk coupling mechanism. Then, based on complex network theory, we construct the incident causation model and revise the node’s centrality with the coupling value. Finally, the network topology parameters are calculated to quantitatively describe the causal characteristics of accidents, revealing the risk evolution process and critical causes. The research results indicate that the key causes of accidents are failure to construct according to regulations, inadequate emergency measures, poor ability of judgment and decision-making, and insufficient understanding of abnormal situations. The front end of critical links is subject to human or management risks and should be carefully controlled during construction.