Online extensive reading has been shown to improve English reading comprehension and related motivational factors. However, few studies have examined the structural relationship between affective variables and reading comprehension in this platform. Thus, this study designed an online extensive reading program to examine this relationship and the affective behavior of a sample of university students. Clustered random sampling was used to select two experimental groups (N = 120, N = 130) and a control group (N = 100), who were requested to take the Test of English as a Foreign Language reading comprehension pre-and post-tests and complete online surveys about self-beliefs, reading motivation, and English reading behavior. Based on the findings, the experimental groups significantly outperformed the control group in reading comprehension. Meanwhile, reading self-efficacy predicted intrinsic and extrinsic motivation, but self-concept only predicted extrinsic drive. Although there was no correlation between extrinsic or intrinsic motivation and English reading comprehension, only the latter mediated self-efficacy with English reading behavior. Surprisingly, reading behavior did not mediate intrinsic motivation and reading comprehension. The findings imply that internal motivation and reading behavior cannot guarantee students' reading comprehension achievement.