To improve the estimation accuracy, a set of models based on ASIF (activity-modal structure-energy intensity-emission factor) methodology were established to evaluate the benefits of energy saving and emissions reduction from container handling equipment upgrades at port terminals, by introducing the ideas of life cycle assessment and cost benefit analysis. Next, the Ningbo-Zhoushan Port was taken for case study. The results show that the container handling equipment upgrades at Ningbo-Zhoushan Port can save 19.11 thousand tons of coal equivalent, reduce 61.75 thousand of tons of carbon dioxide, and cut 69.6 millions Yuan RMB of annual average cost. In addition, neglecting energy’s well-to-wheel (WTT) emissions would significantly affect the accuracy of CO2 emissions reduction, with a 8.65% of underestimation or a 40.83% of overestimation. The cost savings would be considerably overestimated by 59.63% without equipment upgrades cost but slightly underestimated by 2.30% without carbon trading cost. Moreover, the potentials of energy saving and CO2 emissions reduction are greatly influenced by container throughput, and the corresponding elasticity coefficients are larger than or equal to 1, respectively. The maximum potential of cost saving results from diesel’s price change, with a elasticity coefficient of 2.73. Consequently, the findings could provide technical support for evaluating the effect of port greening policies on energy saving and emissions reduction.