To improve efficiency and keep an edge in today’s increasingly competitive global business environments, this study aims to integrate resource allocation and task assignment for optimizing the cost and maximum throughput of business processes with many-to-many relationships between resources and activities using numerical analysis approaches and improved genetic algorithm. Firstly, a formal business process model for analyzing cost and maximum throughput is presented based on set theory. Secondly, the mathematic models of integrating resources allocation and task assignment for optimizing the cost and maximum throughput of business process are proposed respectively and solved by the improved genetic algorithm. Finally, the effectiveness and viability of the proposed methods are verified in numerical and practical cases respectively.