A computational study has been performed for various options of the thorium reactor core loading. Neutronic studies of fuel have been conducted, its isotopic composition has been calculated, and the alpha emitters and the sources of neutron and photon radiation in the microencapsulated nuclear fuel have been analyzed. The studies had the purpose of developing the methodology used to estimate the radiation characteristics of nuclear fuel with a complex inner structure. Emphasis is placed on calculating the quantitative and spectral composition of the neutrons formed as the result of (a, n) reactions on small- and average-mass nuclei. The ratio of the quantity of the neutrons resulting from the (a, n) reactions to the quantity of the neutrons formed as the result of spontaneous fission has been calculated for fuel with heterogeneous and homogeneous arrangements of fissionable and structural elements. The developed tools will make it possible to estimate the neutron radiation dose, to revise the traditional fresh and spent fuel handling procedures, and to estimate, using the Rossi alpha method, the neutron multiplication factor in deeply subcritical systems. The neutron yield and spectrum were calculated using an analytical model and verified codes such as WIMS-D5B, ORIGEN-APP, SOURCES-4C and SRIM-2013.