Despite the huge number of studies on control-display compatibility conducted over the past fifty years, there are still debates concerning the efficacy of conventional measures such as subjective evaluation and performance measures for discriminating between compatible and incompatible control-display mappings. Since compatibility refers to the control-display relationship corresponding to mental model of the users, we tried to apply functional neuroimaging technique as a direct objective measure for analyzing cognitive factors involved in human-machine interaction (HMI). Functional Magnetic Resonance Imaging (fMRI) was applied in order to analyze rotary control-linear display movement compatibility for horizontal and vertical linear displays. Although the results of behavioral measures were not significantly different for incompatible and compatible control-display mappings, neuroimaging results were quite successful in discriminating between them. Moreover, the fMRI results showed significantly greater brain activity for the incompatible condition than for the compatible one in the left posterior cingulate and the right inferior temporal gyrus that reveals the involvement of a greater cognitive load in terms of attention and visuomotor transformation in the incompatible condition. The results of this study suggest that neuroimaging method is a good complement to conventional measures and is quite helpful to acquire a better understanding of the cognitive processes involved in HMI.