As an important coastal protective structure, the breakwater is prone to failure due to foundation damage under seismic actions. However, the seismic performance evaluation of breakwaters has received little attention. This study conducts a seismic fragility analysis of composite breakwaters constructed on liquefiable foundations. By adopting a performance-based seismic design (PBSD) approach and considering the record-to-record (RTR) variability of ground motions, the seismic performance of the breakwaters is assessed over their entire lifecycle. Based on the results of the parameter sensitivity analysis, the reinforcement schemes were proposed in terms of delaying foundation liquefaction and limiting the lateral displacement of liquefied soil. The results of the seismic intensity measure (IM) parameter selection indicate that the commonly used peak ground acceleration (PGA) exhibits a weak correlation with the seismic response of the breakwater, whereas the cumulative absolute velocity (CAV) has a strong correlation. The comparison of the reinforcement schemes shows that the Dense Sand Column (DC) scheme provides significant reinforcement effects, while the Concrete Sheet Pile (CSP) scheme is more suitable for reinforcing existing breakwaters. The seismic performance assessment framework can also be applied to other structures where structural damage is closely related to foundation deformation, such as caisson quays and embankments.