In this paper, a tomography approach aiming at reconstructing a phase-space structure is proposed. For the phase-space resolved diagnostic system, a signal must be decomposed in real-space, velocity-space, and time; therefore, it is challenging to obtain a sufficiently high signal intensity in a single detector bin. To overcome this difficulty, three different sets of data having different integration directions in real-space, velocity-space, and time are simultaneously used, and a reconstruction of the original structure in the phase-space is attempted by a tomographic manner. The proposed method is demonstrated using a synthetic dataset in the actual diagnostic setup in the Large Helical Device. Time evolution of a phase-space perturbation induced by the Landau damping, which is caused by energetic particle-driven magnetohydrodynamic bursts, is successfully reconstructed by this method. Robustness against realistic diagnostic noise is also presented.