The regulation for emission gas of the motorcycle is rapidly being strengthened as the concern about global environment grows around the world, and manufacturers are facing the problem to reduce the toxic materials in the emission gas more. As the technology to reduce the toxic materials, it is common to install a three way catalyst (TWC) on an exhaust system and optimize the oxygen concentration at the inlet of TWC by maintaining air fuel ratio (A/F) on stoichiometric A/F with the control of fuel injection quantity. Furthermore, TWC itself is designed to maintain proper oxygen concentration by the addition of a substance with oxygen storage capacity (OSC), which is able to suppress the variation of the oxygen concentration. However, TWC losses OSC during transient operation with the effect of a large disturbance of A/F and the conversion efficiency of TWC is not able to recover right after the disturbance even though maintaining the A/F near the stoichiometric A/F, which is regarded as a future problem. Therefore the authors focused on maintaining OSC properly with A/F control in order to solve the above problem, which means that the model which estimates the amount of stored oxygen by using the A/F at the inlet of TWC was developed and applied to A/F controller. This controller was applied to a motorcycle and its effectiveness was tested, then the result was found that the controller improved the conversion efficiency of TWC and reduced the toxic materials more during the transient operation.