Variation in several brain regions and neural parameters is associated with intelligence. In this study, we adopted functional connectivity (FC) based on Brainnetome-atlas to predict the intelligence quotient (IQ) scores quantitatively with a prediction framework incorporating advanced feature selection and regression methods. We compared prediction performance of five regression models and evaluated the effectiveness of feature selection. The best prediction performance was achieved by ReliefF+LASSO, by which correlations of r=0.72 and r=0.46 between prediction and true values were obtained for 174 female and 186 male subjects respectively in a leave-one-out-cross-validation, suggesting that for female subjects, a better prediction of IQ scores can be achieved using precise FCs. Further, weight analysis revealed the most predictive FCs and the relevant regions. Results support the hypothesis that intelligence is characterized by interaction between multiple brain regions, especially the parieto-frontal integration theory implicated areas. This study facilitates our understanding of the biological basis of intelligence by individualized prediction.