Three-dimensional quantitative structure-activity relationship (3D-QSAR) method is introduced for the first time into the structure-performance study of organic sensitizers using topomer comparative molecular field analysis (Topomer CoMFA). A total of twenty-three phenothiazine derivatives was utilized to establish the 3D-QSAR model. The generated Topomer CoMFA model is statistically significant with the leave-one-out correlation coefficient (q(2)) of 0.698 and the non-cross-validated correlation coefficient (r(2)) of 0.966, respectively. The theoretically predicted power conversion efficiencies (PCE) match well with the experimentally observed values, verifying the high predictive ability of the Topomer CoMFA model. Molecular field information (i.e., electrostatic and steric fields) of the substituted phenothiazines was analysed in detail. The structural modification of substituted phenothiazines has been performed and novel phenothiazine derivative with theoretically improved PCE has been proposed. The resulting Topomer CoMFA model in this work could provide a new perspective and offer new insights into the structure-performance relationship of dye sensitizers and potentially facilitate the rational design, selection and prediction of as yet unsynthesized organic sensitizers for the dye-sensitized solar cells.