We performed a benchmark study for 58 cases (22 cases reported in this paper and 36 cases reported in online as supplementary materials of this paper) using the recent version (version 2.88) of the Particle and Heavy-Ion Transport code System (PHITS) in the following fields: (1) particle production cross-sections for nuclear reactions from 20 MeV to 1 GeV, (2) thick-target neutron yields and neutron shielding, (3) depth-dose distribution in water using C-12 beam, and (4) electron and photon transportation over a wide-energy range from keV to GeV. Overall agreements were found to be sufficiently satisfactory; however, several discrepancies are observed, particularly in particle productions with energies below 100MeV, neutron production for Li-7(p,n)Be-7, and photonuclear reactions. To overcome these inaccuracies and to further improve the code, it will be necessary to incorporate a high-energy version of the evaluated nuclear data library JENDL-4.0/HE and the photonuclear data file JENDL-PD in the PHITS package.