Due to the low boiling point of helium, the nitrogen-rich off gas of the nitrogen rejection unit (NRU) in the liquefied natural gas (LNG) plant usually contains a small amount of CH4, approximately 1-4% He, and associated gases, such as H2. However, it is difficult to separate hydrogen and helium. Here, we propose two different integrated processes coupled with membrane separation, pressure swing adsorption (PSA), and the electrochemical hydrogen pump (EHP) based on different sequences of hydrogen gas removal. Both processes use membrane separation and PSA in order to recover and purify helium, and the EHP is used to remove hydrogen. The processes were strictly simulated using UniSim Design, and an economic assessment was conducted. The results of the economic assessment show that flowsheet #2 was more cost-effective due to the significant reduction in the capacity of the compressor and PSA because of the pre-removal of hydrogen. Additionally, using the response surface methodology (RSM), a Box-Behnken design experiment was conducted, and an accurate and reliable quadratic response surface regression model was fitted through variance analysis. The optimized operating parameters for the integrated process were determined as follows: the membrane area of M101 was 966.6 m2, the permeate pressure of M101 was 100 kPa, and the membrane area of M102 was 41.2 m2. The maximum recovery fraction was 90.66%, and the minimum cost of helium production was 2.21 $/kg. Thus, proposed flowsheet #2 has prospects and value for industrial application.