To address the challenge of certain rail transit lines facing closure due to continuously declining ridership, this study takes the evolutionary trajectory of Japan's rail transit development as a starting point and employs a multi-case comparative analysis. The research thoroughly investigates the triggering factors, policy frameworks, and supporting measures for the closure of low-ridership lines. The results show that changes in population and industrial structure, as well as shifts in travel modes, are the core factors leading to the sustained decline in rail transit ridership. At the same time, increased maintenance costs caused by aging infrastructure and severe revenue-expenditure imbalances have further worsened line operations. In response, Japan has established evaluation systems centered on transport density to classify and assess low-ridership lines, and has implemented systematic governance schemes covering ridership cultivation and cost control. For lines where closure is unavoidable, innovative alternatives such as Bus Rapid Transit (BRT) dedicated lanes and demand-responsive transit have been adopted, effectively addressing operational challenges and ensuring residents’ basic mobility needs. By comprehensively analyzing the problem of low-ridership rail transit closures and the corresponding measures taken in Japan, this study summarizes relevant experiences and lessons, aiming to provide references for the future operation and transformation of rail transit in China.