Conventional studies on the reading processes of Japanese learners have based their results on the scores of post-reading tests. However, these tests only measure the reading process via an offline method and thus do not reflect the cognitive aspect of the reading process. Therefore, this study investigated an online cognitive process of oral reading by Chinese students learning Japanese by measuring eye movements during reading. The independent variables were the type of instruction and working memory capacity. There were two types of instructions: those based on content comprehension and those on reading speed. The dependent variables were the post-reading test score, reading time, total fixation time and fixation time for important idea units. The eye-movement measurement results showed that the type of instruction affected the reading process, thus affecting overall comprehension, as shown in the post-reading test scores. When compared with the reading speed instructions, the content comprehension instructions produced a greater improvement in attention to details, which was reflected in a longer reading time, total fixation time and fixation time for important idea units. Furthermore, the effect of working memory capacity differed according to the types of instructions. Learners with larger working memory capacity paid more attention to detail in the content comprehension instruction group, with a longer reading time and paying greater attention to important details.