The benchmarking of CO2 emissions serves as the foundation for the accurate assessment of the environmental impact of air traffic. To calculate the environmental benchmarks of arrival traffic flows with Point Merge System (PMS) patterns, this study proposes a 4D trajectory optimization method that combines data-driven and optimal control models. First, the predominant arrival routes of traffic flows are identified using the trajectory spectral clustering method, which provides the horizontal reference for 4D trajectory optimization. Second, an optimal control model for vertical profiles with point merging topology is established, with the objective of minimizing the fuel–time cost. Finally, considering the complex structure of the PMS, a flexible and adaptable genetic algorithm-based vertical profile nonlinear optimization model is created. The experimental results demonstrate that the proposed method is adaptable to variations in aircraft type and cost index parameters, enabling the generation of different 4D trajectories. The results also indicate an environmental efficiency gap of approximately 10% between the actual CO2 emissions of the arrival traffic flow example and the obtained benchmark. With this benchmark trajectory generation methodology, the environmental performance of PMSs and associated arrival aircraft scheduling designs can be assessed on the basis of reliable data.