Absorption of H2S is one of the important part in biogas purification.. This process requires a purification system to reduce the content of harmful gas. The maximum tolerance of H2S content for biogas generator set input is 5 ppm, while measured input of H2S in cow manure has a concentration range from 43 to 45.5 ppm. Therefore, it needs proper optimization design to represent the performance of the purification system. Particle Swarm Optimization refers to the process of identifying the best element (according to one or more user-specified criteria) among a set of possible alternatives. In this research, we compare the results from modeling plant and experimental plant in order to the reaction and mass at the biogas purification plant. Based on the experiment plant, measurement of produced biogas shows the reduction of H2S concentration up to 94.5% and produce H2S with concentration of 0.55 ppm. Meanwhile, in modified plant model the reduction of H2S is up to 94.44% with the gas concentration of 0.53 ppm. Validation of plant model has showed the data trend that approaches the measurement results of experimental plant with an average of absolute error of 0.018, respectively.