We present a multi-objective analysis of the optimization of seawater reverse osmosis (RO) desalination systems, considering economic, power requirement, and exergo-economic factors. Exergy flow for each stream and exergy destruction for each equipment in the RO network is included in the model. The exergo-economic unit cost (EUC) for the final product is considered as an objective function. An enhanced version of the augmented epsilon constraint method, AUGMECON2, is utilized to solve the multi-objective optimization problem, which allows for lexicographic optimization for other objectives if alternative optimum solutions exist. Redundant iterations are avoided through the use of the bypass coefficient. Results show that the Pareto solutions for permeate split design are located below the normal design. Fixed cost dominates the exergo-economic unit cost. The power cost has the greatest share of water cost, while pass 1 has the greatest share of exergy destruction. The throttling valves and blending of different salinity streams (final product mixer and first pressurization stage mixer) could cause non-negligible exergy destruction. The fixed cost for each equipment, exergy rate, and EUC for each flow rate are analyzed, in order to provide insights into the system.