There were two purposes in the study. One was to explore the cognitive activities during spatial problem solving and the other to probe the relationship between spatial ability and science concept learning. Twenty university students participated in the study. The Purdue Visualization of Rotations Test (PVRT) was used to assess the spatial ability, whose items were divided into different types of problems with respect to the rotation angles and levels of plane invisibility. The eye tracking technology and the interview technique were employed to analyze subjects' the online cognitive processes and problem solving strategies. Students' concept gains were examined by content analysis after reading a science report. The result shows that, first, the interview analysis shows that students of different PVRT performances employed different problem solving strategies. Second, rotation angles as well as levels of plane invisibility inserted significant effects on the online processes and performances of the spatial problem solving. Third, the accuracy performance of PVRT was correlated with eye movement patterns. At last, it was found that concept performance was not correlated with PVRT performance but associated with spatial memory and problem solving strategies.