Summary: The aim of this paper is to optimize the benchmarks and prioritize the variables of decision-making units (DMUs) in data envelopment analysis (DEA) model. In DEA, there is no scope to differentiate and identify threats for efficient DMUs from the inefficient set. Although benchmarks in DEA allow for identification of targets for improvement, it does not prioritize targets or prescribe level-wise improvement path for inefficient units. This paper presents a decision tree based DEA model to enhance the capability and flexibility of classical DEA. The approach is illustrated through its application to container port industry. The method proceeds by construction of multiple efficient frontiers to identify threats for efficient/inefficient DMUs, provide level-wise reference set for inefficient terminals and diagnose the factors that differentiate the performance of inefficient DMUs. It is followed by identification of significant attributes crucial for improvement in different performance levels. The application of this approach will enable decision makers to identify threats and opportunities facing their business and to improve inefficient units relative to their maximum capacity. In addition, it will help them to make intelligent investment on target factors that can improve their firms’ productivity.