This study aims to investigate the effects of the centralized allocation and optimization of Taiwan’s railway resources (personnel and equipment) on the overall operational efficiency of its railway industry, based on the concept of two-phase centralized allocation and reallocation of resources. A Taiwan railway data analysis conducted in 2011 showed that the high overall output due to the efficient allocation of resources has led to large-scale organizational changes and adjustments (such as staff reduction) in Taiwan’s railway industry, resulting in widespread organization resistance. Therefore, this study divides resource allocation into long-, middle-, and short-term allocation, with two resource adjustment programs according to different ranges and ways of resource allocation. This process can enable Taiwan’s railway industry to achieve balance between output and organization resistance under different environments in a more efficient manner.