Membrane desalination technologies such as reverse osmosis (RO) are being widely used around the world to deal with the growing freshwater shortage. In addition, the use of new reverse osmosis technologies that improve the performance of traditional ones, has received more attention. The main problem in desalination plants is the high total specific energy consumption as well as high capital investment, maintenance and repair costs. In this study, the performance of a new closed-circuit reverse osmosis (CCRO) desalination system with side-conduit as a replacement for energy recovery device, is investigated based on energy, exergy and exergoeconomic (3E) analysis. 3E analysis is performed based on four important factors including 1) concentration of inlet feed water 2) number of cycles 3) osmotic pressure 4) mass flow rate of feed water. Then, using the output data obtained from 3E analysis, the optimal points for six key parameters of exergy efficiency, net driving pressure (NDP), total unit cost product (SUCP), mass flow rate of permeate, recovery ratio and specific energy are determined through multi-objective optimization. The simulation results show that in the proposed system, by increasing the number of cycles, the recovery ratio increases while the system costs also increase due to increase in pressure and concentration of inlet feed. It is found that the optimal recovery ratio of 64.29% is obtained for 9th cycle and inlet feed concentration of 6.95% and the optimal specific energy consumption of 2.5 kWh/m3 is obtained for 7th cycle and inlet feed concentration of 6.07%.