In order to ensure the operational safety of the project of the Chengdu Metro Line 13 crossing the pile foundations of the Jiaozi overpass, the construction safety risks of the shield tunnel crossing the bridge pile foundation group are evaluated. Firstly, the fuzzy analytic hierarchy process (FAHP) combined with grey relational analysis (GRA) is used to conduct a multilevel and multifactor safety risk assessment. Based on the actual construction characteristics and the construction process of crossing pile foundation groups, a reasonable safety risk assessment index system for shield tunnel crossing urban overpass pile foundations is established, and factors with a relatively high degree of safety risk impact are selected. Then, the analysis results are compared with field test data to verify the reliability of the safety risk assessment. Results indicate that during the construction process of shield tunneling crossing bridge pile foundations, the pile foundation replacement construction technology and shield tunneling underpass construction have the greatest impact in the first layer of factors. The original bridge pier and the connection between the bearing platform and the replacement beam have the greatest impact in the second layer of factors. The risk assessment results are in accord with the engineering practice. Based on the assessment results, key control and full process monitoring measurements are implemented for the pile foundation replacement construction. The applicability and reliability of risk assessment method are verified by the monitoring results.