This article is concerned with the multitask multiagent allocation problem via many-objective optimization for multiagent systems (MASs). First, a novel layered MAS model is constructed to address the multitask multiagent allocation problem that includes both the original task simplification and the many-objective allocation. In the first layer of the model, the deep Q-learning method is introduced to simplify the prioritization of the original task set. In the second layer of the model, the modified shift-based density estimation (MSDE) method is put forward to improve the conventional strength Pareto evolutionary algorithm 2 (SPEA2) in order to achieve many-objective optimization on task assignments. Then, an MSDE-SPEA2-based method is proposed to tackle the many-objective optimization problem with objectives including task allocation, makespan, agent satisfaction, resource utilization, task completion, and task waiting time. As compared with the existing allocation methods, the developed method in this article exhibits an outstanding feature that the task assignment and the task scheduling are carried out simultaneously. Finally, extensive experiments are conducted to: 1) verify the validity of the proposed model and the effectiveness of two main algorithms and 2) illustrate the optimal solution for task allocation and efficient strategy for task scheduling under different scenarios.