The reading comprehension of geometry proofs necessitates a coherent mental representation of all the information conveyed in the figure and text. Eye movements can be used to assess the perceptual and cognitive processes, and how colored figures affect the integration of text and figures during comprehension. For our experiment, we used four junior high school level geometry proofs with colored/uncolored figures to examine 31 undergraduate students who had learned but have not mastered geometry proofs. First, the participants’ eye movements were recorded during reading. A paper-and-pencil recall test was then administered to the participants after the reading procedure. The data reveal that half of the fixations were located on figures, and the proportion of fixations to the pixels of the figures was greater than that of the texts. The results suggested that the reading of geometry proofs depended more on figures that organized the statements using a specific status and provided cues for the geometry proof properties compared to text. Working memory limitations increased the regression time for figures. Additionally, figures provided utility cues for recalling geometric properties, which assisted readers in performing deductions and verifications. Colored figures influenced the visualization of undergraduate students when reading geometry proofs. This reduced the initial reading comprehension time of one theorem, but did not affect the regression time and comprehension exhibited in the recall tests. Valid analyses of eye movements when reading geometry proofs must be supported by definitions of mathematical words and data-screening skills.