ESI, based on SCI and SSCI, plays an important role in world-class universities and subjects evaluation and attracts broad attentions from domestic universities. Under this background, we discussed the six problems in world-class universities and subjects evaluation using ESI, such as the differences between the method of output allocation in ESI and that used in general in China; the different retrieval results for the same evaluation objects. On the basis of these problems, corresponding solutions were put forward, such as accurately grasping the connotation of indicators, result shows, baselines and thresholds, and retrieval methods; further valuing the discovery of high-level papers and scientific elites.