While more and more digital-based texts have been to a great extent replacing paper-based texts in the modern reader’s reading activity, the use of digital annotation system could significantly revolutionize the reader’s reading habits. This research aims to clarify how cognitive style and annotation quality may affect reading performance while a digital annotation tool is applied to reading activity. Research results show that most annotations made by our research subjects mainly fall under the category of “simple annotation,” which consists of a large amount of translations and textual explanations. The finding implies that the general reader’s reading of texts written in foreign languages tends to focus on vocabulary comprehension as their top priority. Our research also discovers that under both categories of “simple annotation” and “integrity annotation,” research subjects belonging to visual-oriented cognitive style show better reading performance than those belonging to verbal-oriented cognitive style. Moreover, research results indicate that while “simple annotation” holds a majority in the reader’s reading activity, this way of applying an annotation tool inversely brings about negative effects on reading performance. Under the circumstances, the reader’s attention is primarily engaged by meanings on the textual surface rather than focused on reflective, analytical, and critical thinking of texts. This tendency towards a superficial reading of texts may logically explain the phenomenon that the general reader’s reading performance has not improved with transitions of educational stages. In view of the negative effects entailed in the limitation caused by applying simple annotations, our study suggests that educators should encourage students to try diverse annotation methods, such as “linking annotation” and “organizing annotation,” in their digital reading activity, for the purpose of motivating them to think deeply and independently as well as to enhance their interactions with critical issues in daily life.