Automatic evaluation of English timing control proficiency is carried out by comparing segmental duration differences between learners and reference native speakers. To obtain an objective measure matched to human subjective evaluation, we introduced a measure reflecting perceptual characteristics. The proposed measure evaluates duration differences weighted by the loudness of the corresponding speech segment and the differences or jumps in loudness from the two adjacent speech segments. Experiments showed that estimated scores using the new perception-based measure provided a correlation coefficient of 0.72 with subjective evaluation scores given by native English speakers on the basis of naturalness in timing control. This correlation turned out to be significantly higher than that of 0.54 obtained when using a simple duration difference measure.