This study aims to investigate the effect of suprasegmental phonological training on connected-text reading comprehension of Chinese university students with different English reading proficiency levels. A sample of 160 freshmen was recruited and randomly divided into experimental and control groups, and the experimental group was given a 12-week training on stress, intonation and rhythm in English. Comparison and analysis of the subjects' reading comprehension performance, involving overall accuracy and speed as well as literal and inferential comprehension, reveal that: (1) suprasegmental phonological training exerts positive effects on the subjects' overall reading comprehension, especially on reading time and literal comprehension; (2) lower-proficiency readers improve more remarkably than higher-proficiency readers in terms of overall accuracy and literal comprehension, while the effect of the training on reading time is significant regardless of the subjects' reading proficiency. The results indicate that with explicit instruction and intensive exposure to suprasegmental knowledge, students' automaticity in lower level processing, such as parsing and understanding propositional messages, can be increased. From a perspective of interaction among different cognitive and psychological processes of reading comprehension, this study can shed light on developing students' reading comprehension in EFL contexts.