Summary: This paper studies a typical kind of efficiency evaluation problem for parallel systems. Firstly, decision making unit (DMU) has two parallel components. Secondly, there exits not only shared input, but also common (undesirable) output between the two components, and the input and shared (undesirable) output between two components cannot be proportionally differentiated with each other. Based on constant and variable returns to scale, this paper analyzes efficiency of the DMU and its components, and puts forward one evaluation method for determining the overall efficiency of the DMU and individual efficiency of each component. This approach can realize efficient allocation of shared resource and (undesirable) output, at the same time, it can also evaluate the system’s efficiency. Finally, a case study of China road transportation industry is presented to demonstrate the approach.