We measured the synchrotron-radiation (SR)-based Mössbauer spectra of Ni-based nanoparticles with a hexagonal structure that were synthesised by chemical reduction. To obtain Mössbauer spectra of the nanoparticles without 61Ni enrichment, we developed a measurement system for 61Ni SR-based Mössbauer absorption spectroscopy without X-ray windows between the 61Ni84V16 standard energy alloy and detector. The counting rate of the 61Ni nuclear resonant scattering in the system was enhanced by the detection of internal conversion electrons and the close proximity between the energy standard and the detector. The spectrum measured at 4 K revealed the internal magnetic field of the nanoparticles was 3.4 ± 0.9 T, corresponding to a Ni atomic magnetic moment of 0.3 Bohr magneton. This differs from the value of Ni3C and the theoretically predicted value of hexagonal-close-packed (hcp)-Ni and suggested the nanoparticle possessed intermediate carbon content between hcp-Ni and Ni3C of approximately 10 atomic % of Ni. The improved 61Ni Mössbauer absorption measurement system is also applicable to various Ni materials without 61Ni enrichment, such as Ni hydride nanoparticles.