The optimized location and allocation of earthquake emergency shelters are critical for improving the resilience of communities. However, the existing disaster shelters location–allocation optimization models usually select new shelters from candidate shelters neglecting the existing or planned shelters. The research into comparisons before and after location–allocation optimization between the current planning scenario (CLA scenario) and the supplementary new candidate shelter scenario (SLA scenario) is thus imperative for disaster risk reduction. This article develops a multi-criteria multi-objective multi-scenario supplemental location–allocation optimization model that addresses the concerns related to optimization comparison based on the above two scenarios and provides a higher degree of realism by integrating multi-criteria evaluation and optimization comparison into location–allocation problems. The solutions obtained under the two scenarios are then compared with a case study in Huairou Science City. The results show that the solution under the SLA scenario is superior to the corresponding CLA scenario regardless of the minimal-distance scheme or the minimal-area scheme. The proposed model is proven to be useful for the location–allocation optimization of earthquake emergency shelters, and the presented results can be used as a reference for balancing the interests of the government and residents during the reconstruction and expansion projects of shelters.