The risk factors in the construction of subway shield tunnels have complex and variable characteristics. To address the impact of these characteristics in the evaluation process, a risk assessment method for subway tunnel shield tunneling through the biogas layer construction using WBS-RBS, AHP combined with cloud models is proposed. The WBS-RBS method is used to analyze the construction risk factors from the construction stage and 4M1E, and 24 risk indicators are identified. Use AHP to calculate the weight of risk indicators. Construction risk assessment model is constructed by cloud model theory to evaluate construction risk. Based on the construction project of Hangzhou–Haining Intercity Railway under biogas layer, this paper verifies the construction risk assessment method of subway tunnel under biogas layer with shield. The case study shows that the construction risk of biogas layer under the shield of Hangzhou–Haining Intercity Railway tunnel is medium risk. This paper provides reference value for the analysis and control of the construction risk factors of biogas layer under the shield of subway tunnel.