To investigate the behavior of reaction products with the reactor heights by the change of upflow velocity, a typical real height USAB reactor was built and experiment was conducted. The flow in the reactor by the upflow velocity was flug flow at low upflow velocity but the flow was completely mixed flow at high upflow velocity. Therefore, the concentration of pH, alkalinity and volatile acid was not so different with reactor heights at high upflow velocity. And comparing with low upflow velocity, the distribution of microorganisms with reactor heights did not show big different at high upflow velocity. The removal efficiency of organic compounds depended on the distribution of microorganisms and it was low at high upflow velocity. It is concluded that the operation of reactor with proper upflow velocity to improve contact with organic compounds and microorganisms is recommended.