As a thickening or stabilizing agent, exopolysaccharide (EPS) can significantly enhance food texture. However, the conventional analytical and screening methods of EPS have been unable to meet the current needs of industrial production, owing to low efficiency and heavy time-consumption. A simple and rapid qualitative/quantitative method is needed to accelerate the selection of high EPS-producing strains. Here, a high-throughput screening (HTS) program for EPS production was established in S. thermophilus by combining Congo red agar method (CRA, primary screening) and microplate colorimetric assay (MPC, secondary screening). The correlation coefficient (R²) between CRA/MPC and the phenol-sulfuric acid assay (a classical EPS quantification method) were 0.779 and 0.862, respectively, suggesting the feasibility of this HTS method. A mutant library (>300 colonies) of S. thermophilus was constructed using ribosome engineering strategy, and EPS-producing mutants with the titer from 50 mg/L to 200 mg/L were rapidly obtained by our developed HTS method, confirming that the HTS method is simple and efficient for the isolation of EPS-producing S. thermophilus. Taken together, this HTS method was developed for rapidly screening of EPS-producing S. thermophilus, which could be a valuable tool not only for the rapid detection of EPS production capabilities, but also for the screening of strain libraries from genetic engineering with desirable characteristics.