The goal of this paper was to design the optimal time-varying operating pH profile in the asymmetric reduction of ethyl 4-chloro-3-oxobutyrate by baker's yeast. Ethyl (S)-4-chloro-3-hydroxybutyrate was produced to reach two important quality indices: reaction yield and product optical purity. The method integrated an orthogonal function approximation and an orthogonal array. The technique used a set of orthonormal functions as the basis for representing the possible profile. The optimal profile could be obtained if the orthogonal coefficients were properly adjusted. The orthogonal array was used to design and analyze the effect of each orthogonal coefficient in order to reach the optimal objective (quality) function. The performance based on the proposed strategy was significantly improved by over 10% compared with the traditional fixed pH or uncontrolled pH values during the reaction. The proposed method can be applied to the required dynamic profile in the bioreactor process to effectively improve the product quality, given good design directions and the advantage of the traditional statistical approach.