In recent years, multimodal transportation has achieved rapid development with the support of the governments and stakeholders. Multimodal transportation is characterized by high transportation efficiency, low transportation cost, energy saving and environmental protection. However, the existing transportation industry development indicators are defined and counted from the perspective of a single subsystem. This contribution establishes a performance evaluation index for three container multimodal transportation subsystem from four aspects: capacity, transportation cost, service quality and sustainable development based on system engineering techniques. In order to fully reflect the differences between the decision-makers' subjective experience and preference and objective information, this contribution uses the combination of Analytic Hierarchy Process (AHP) and entropy method to determine the weight of indexes. The methodology is applied to examine performance of three container multimodal transportation subsystems in Ningbo-Shaoxing (China) multimodal transportation system. The results show that: multimodal railway is superior to highways and multimodal inland waterway. The methodology and discussion of the AHP-entropy method may be useful for similar transport systems in a make decision framework.