Abstract: Pichia Pastoris was used as the strain for rhamnosidase fermentation.A structured kinetic model was used to establish an optimization problem.According to the extremum theory of functional, the optimization problem has been converted to solving differential-algebraic equation (DAE) problem.Set the multipliers by iteration loops to solve the DAEs and obtain an optimal methanol feeding curve.Practice has proved that this method improved the yield of rhamnosidase expression in Pichia Pastoris fermentation system.