Many studies have concluded that question generation has a positive effect on students' reading comprehension. However, few studies have delineated how students generate questions from a text and what processes are involved in question generation. This study aims to investigate how the question generation processes improve students' reading comprehension, using an online question generation system including the organisation, composition and peer assessment modules. 19 out of 106 non-English major college students were recruited as participants. They were required to complete question generation tasks in the organisation, composition and peer assessment modules. Students' scores on the pre-and post-tests, action logs in the online question generation system, and interview transcripts were collected and analysed. In a micro view, results of this study indicated that college students who showed more progress in reading comprehension demonstrated similar question generation patterns. In the organisation module, those who made more progress had a higher frequency of adding new vocabulary, sentences, and main ideas and editing their previously organised information. In the composition module, they had a higher frequency in reviewing the previously organised information from a text to generate questions and in editing the organised information. In the peer assessment module, those who showed more progress were much more active in viewing peers' questions, providing comments on peers' questions, reading and responding to peers' comments on the questions. In a macro view, the intensive engagement and the actions of editing to retrieve the organised information to compose the online questions and reviewing peers' questions online were found to be critical factors for enhancing students' reading comprehension.