The present study investigated (a) whether the perceived cognitive load was different when geometry problems with various levels of configuration comprehension were solved and (b) whether eye movements in comprehending geometry problems showed sources of cognitive loads. In the first investigation, three characteristics of geometry configurations involving the number of informational elements, the number of element interactivities and the level of mental operations were assumed to account for the increasing difficulty. A sample of 311 9th grade students solved five geometry problems that required knowledge of similar triangles in a computer-supported environment. In the second experiment, 63 participants solved the same problems and eye movements were recorded. The results indicated that (1) the five problems differed in pass rate and in self-reported cognitive load; (2) because the successful solvers were very swift in pattern recognition and visual integration, their fixation did not clearly show valuable information; (3) more attention and more time (shown by the heat maps, dwell time and fixation counts) were given to read the more difficult configurations than to the intermediate or easier configurations; and (4) in addition to number of elements and element interactivities, the level of mental operations accounts for the major cognitive load sources of configuration comprehension. The results derived some implications for design principles of geometry diagrams in secondary school mathematics textbooks.