This paper addresses the Multi-Skill Resource-Constrained Project Scheduling Problem with Transfer Times (MSRCPSP-TT). A new model has been developed that incorporates the presence of transfer times within the multi-skill RCPSP. The proposed model aims to minimize project’s duration and cost, concurrently. The MSRCPSP-TT is an NP-hard problem; therefore, a Multi-Objective Multi-Agent Optimization Algorithm (MOMAOA) is proposed to acquire feasible schedules. In the proposed algorithm, each agent represents a feasible solution that works with other agents in a grouped environment. The agents evolve due to their social, autonomous, and self-learning behaviors. Moreover, the adjustment of environment helps the evolution of agents as well. Since the MSRCPSP-TT is a multi-objective optimization problem, the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) is used in different procedures of the MOMAOA. Another novelty of this paper is the application of TOPSIS in different procedures of the MOMAOA. These procedures are utilized for: (1) detecting the leader agent in each group, (2) detecting the global best leader agent, and (3) the global social behavior of the MOMAOA. The performance of the MOMAOA has been analyzed by solving several benchmark problems. The results of the MOMAOA have been validated through comparisons with three other meta-heuristics. The parameters of algorithms are determined by the Response Surface Methodology (RSM). The Kruskal–Wallis test is implemented to statistically analyze the efficiency of methods. Computational results reveal that the MOMAOA can beat the other three methods according to several testing metrics. Furthermore, the impact of transfer times on project’s duration and cost has been assessed. The investigations indicate that resource transfer times have significant impact on both objectives of the proposed model.