To seek a good balance between efficiency and fairness in emergency relief supply allocation, a high-dimensional multi-objective adaptive allocation algorithm based on two-dimensional integer encoding was developed. First of all, a high-dimensional multi-objective optimization model was constructed with the consideration of total emergency response time, panic degree of the victims, unsatisfactory degree of relief supplies, fairness of supply allocation, loss of the victims, and total cost of emergency response. Then, two-dimensional integer encoding and Adaptive Individual Repair (AIR) were adopted to resolve potential emergency resource conflicts. Finally, the shift-based density estimation and Strength Pareto Evolutionary Algorithm 2 (SPEA2) were introduced to design a high-dimensional multi-objective allocation algorithm for disaster relief supplies. Simulation results show that compared with Encoding Repair and Non-dominated Sorting based Differential Evolution algorithm (ERNS-DE) and Greedy-Search-based Multi-Objective Genetic Algorithm (GSMOGA), the proposed algorithm had coverage values increased by 34.87%, 100% and 23.59%, 100% in two emergency environments, respectively. Moreover, the hypervolume values of the proposed algorithm were much higher than those of the two comparison algorithms. Experimental results verify that the proposed model and algorithm allow decision makers to select emergency schemes according to actual emergency needs, and have better flexibility and efficiency.