There are significant differences in passenger flow distribution patterns between metropolitan rapid rail transit and metro systems. How to conduct a scientific and reasonable evaluation is crucial to the healthy development of metropolitan areas and urban agglomerations in China, and thus deserves in-depth exploration. This paper systematically defines the connotation, calculation methods, and applicable boundaries of passenger transport intensity and passenger flow density based on the Urban rail transit operation indicator system (GB/T38374—2019) and the 2025 annual statistical data of the China Urban Rail Transit Association. It compares and analyzes the differences between metropolitan rapid rail transit and metro in terms of travel space, time, demand, and operational characteristics. Using data from 34 operational metropolitan rapid rail transit in 22 cities across the country and typical lines in multiple cities as examples, this paper conducts a quantitative empirical analysis. The results show that in 2025, the average passenger transport intensity of medium-capacity system category including metropolitan rapid rail transit in China was only 1.8 thousand person-times/km·day, far lower than the 7.3 thousand person-times/km·day for metro systems, while the passenger flow density reached 24.6 thousand person·km/km·day, indicating that its transport efficiency was underestimated. The average travel distance of metropolitan rapid rail transit is generally greater than 30 km, which is the core factor causing the evaluation deviation between the two indicators. Passenger flow density is more capable of matching the functional positioning of long-distance transportation of metropolitan rapid rail transit. The passenger flow density indicator is also applicable to metro lines with shorter travel distances in central urban areas, but due to the relatively short average travel distance of metro, passenger transport intensity and passenger flow density are highly positively correlated. Building on a systematic review of existing studies, this paper proposes a multi-dimensional evaluation framework for metropolitan rapid rail transit, with passenger flow density as its core while incorporating average travel distance and spatiotemporal convergence benefits. The objectivity of the proposed framework is validated through theoretical analysis, empirical testing, and comprehensive benefit assessment. Optimization recommendations are further offered to provide theoretical support and reference for the planning approval, operational assessment, and high-quality sustainable development of metropolitan rail transit.