Previous studies have evaluated reading comprehension as the general understanding of reading texts. However, this broad and generic assessment of reading comprehension overlooks the specific aspects and processes that students need to develop. This study adopted Kintsch's Construction-Integration model to tap into reading comprehension at different levels and investigated how English as a foreign language (EFL) students benefit from online annotations to scaffold reading comprehension. Fifty EFL students participated in this study and the data collected included (1) the pre- and post-test assessments in reading comprehension levels, (2) the students' online annotations on reading texts, and (3) the discussion transcripts from an online discussion forum. The results from the first two data sources (1 and 2) were the data-sets used to investigate the influence of the annotation types on reading comprehension levels. The third data source was the data-set used to probe into the process of how students benefited from annotation types to reach different levels of reading comprehension. Four types of online annotations were frequently used by the students while reading online, including (1) marking vocabulary, (2) adding Chinese explanatory notes to unknown vocabulary, (3) marking text information, and (4) adding summary notes to each paragraph. Different frequencies of using the four types of online annotations resulted in three different comprehension levels: surface-based, text-based, and situation-based levels. Marking vocabulary and adding Chinese explanatory notes helped scaffold the students' learning to achieve surface comprehension levels to facilitate recognition and meaning of unknown vocabulary. Marking text information and in particular, the adding of summary notes to each paragraph were the core annotations that helped students comprehend the online text in text-based and situation-based levels. EFL teachers can guide students to use online annotations to different extents in order to deepen their reading comprehension.