Produced natural gas from well can not be used directly as fuel or raw material. Raw natural gas contain some impurities such as water, solid, H2S and CO. Usually, CO2 separation utilize amine column absorber, dehydration, LPG extraction and dew to separate natural gas from CO2. The new gas separation technology is SuperSonic Separation (3S) that combining Joule Thomson Valve and Turbo Expander technologies. 3S design model was built using material balance equation, energy balance and Bernoulli law. In this research, new stochastic optimization algorithm namely Rain Water Algorithm, is used. Selected optimized variables are diameters and length of pipe i.e. input diameter, diameter at laval nozzle, diameter after naval nozzle, pipe length on static vanes to laval nozzle and length of pipe from laval nozzle to cyclonic separation. These variables will affect to both gas velocity and cost of system design. The optimization result using RWA shows the targetted velocity (ut = 540.3 m/s) was obtained at optimized variable of diameter before laval nozzle 0.2428 m, diameter at laval nozzle 0.0117 m, diameter at cyclonic separation 0.0289 m, length before laval nozzle 0.1977 m and length after laval nozzle 0.2105 m or in volume is 6.63 × 10-4 m3. The cost of material for decisioned design of 3S is 387.41 USD.