NGC 1275 has been known as a ppint-like X-ray source with a continuum and a Fe-K line. Unlike radio and GeV/TeV gamma-ray emissions, origin of X-ray emission is not yet understood; is it a jet emission like blazars or an accretion corona emission like Seyfert galaxies. X-ray emission is important to determine the SED of jet emission to constrain jet parameters and also understand the relation between accretion and jet. Here we report a recent X-ray probing of NGC 1275 nuclear region with Hitomi/SXS, Swift/XRT, and Suzaku/XIS. Hitomi/SXS gave the first opportunity to measure a Fe-K line of AGNs with several eV resolution. The line center is consistent with the neutral iron emission, and the width is constrained to be 500-1600 km/s (FWHM). This ruled out the origin of broad line region and inner accretion disk. A low-covering-fraction molecular torus or a rotating molecular disk around pc scales, illuminated by accretion corona emission, is suggested as a possible origin. For the continuum emission, Suzaku/XIS monitor observations revealed that the X-ray flux has gradually increased as the GeV gamma-ray flux. Swift/XRT showed a several-days flux increase, associated with the GeV gamma-ray flare. These results on the continuum emission suggests a contribution of jet emission to the X-ray emission. Based on the combined results of Fe-K line and continuum, we discuss some scenarios for X-ray emitting region.