Abstract: In order to comprehensively and scientifically evaluate the degree of public transportation in the process of intercity railway public transportation transformation, this paper was based on the perspective of interconnectivity, started from the connotation and constituent elements of public transportation, established technical indicators that reflect the characteristics of public transportation, and based on this, constructed evaluation indicators with clear value ranges, ideal values, and evaluation standards, formed a multi-level structure of intercity railway public transportation operation evaluation index system. Regarding this evaluation index system, the paper designed a public transportation operation evaluation method including standardized measurement processing of indicator items based on ideal values, multi-level indicator weight calculation, overall evaluation of public transportation operation plans, and calculation of public transportation bottlenecks. The comprehensive evaluation and comparative analysis of the transformation plan for the intercity railway system consisting of the Dongguan-Huizhou intercity railway and the Guangzhou-Dongguan-Shenzhen intercity railway in the Guangdong Hong Kong Macao Greater Bay Area indicate that, the bottlenecks in the current operation plan, including the average passenger flow stop to stop service ratio, maximum section full load rate, and transfer time ratio coefficient, have been significantly improved in the renovation plan. This evaluation method can provide reference for the operation evaluation of other intercity railway systems.