The characteristic identification of the functional materials is important in predicting the performance of a breeding blanket, which is one of the main components of the fusion power plant. The functional materials of the solid-type ceramic breeding blanket are mainly used in the form of pebble beds. Various experimental methods such as laser flash, hot wire, and hot disk method have been utilized to assess the thermal properties of the pebble bed. In recent years, numerical techniques have been also introduced to evaluate mechanical characteristics as well as thermal characteristics of pebble beds. In this study, the mechanical and thermal behaviors of the binary-sized pebbles in a cuboidal container are simulated considering the contact interaction of the pebbles by means of discrete element method. Through a series of numerical simulations of pouring the pebbles into the vibrating container, we investigate the effect of the size difference of the binary-sized pebbles on the packing structures of the pebble beds. The connectivity of binary-sized pebbles is also discussed in terms of the average contact force of the pebbles. Furthermore, heat conduction between the pebbles is considered based on the packing configurations obtained from the mechanical analysis, and the thermal properties of the pebble beds are qualitatively evaluated in terms of the effective thermal conductivity of the pebble beds.