We have developed a molecular dynamics (MD) simulation method to investigate the sintering of nickel nanoparticles in the nickel and yttria-stabilized zirconia (Ni/YSZ) anode of a solid oxide fuel cell (SOFC). The conventional sintering model consists of only two or three nickel nanoparticles. Therefore, it does not reflect the properties of the porous structure of the Ni/YSZ anode or reproduce realistic sintering. Our Ni/YSZ multi-nanoparticle MD simulation method uses a multi-nanoparticle model based on the porosity and Ni/YSZ nanoparticle ratio of a realistic anode. The Ni and YSZ nanoparticles are packed randomly in the simulation cell, and compressed to achieve the correct porosity. Furthermore, because the reliable potential parameters for MD simulation between nickel and YSZ have not been reported, we determine reliable interatomic potential parameters between nickel and YSZ by using the nonlinear least-squares method to fit the Morse potential function to interaction energies obtained by density functional theory. The sintering simulation using our Ni/YSZ multi-nanoparticle model and our potential parameters reveal that the YSZ nanoparticle framework suppresses the sintering of nickel nanoparticles by disrupting the growth of the neck between two nickel nanoparticles. The previously reported model of two nickel nanoparticles did not produce these results. Our multi-nanoparticle MD simulation method is effective for investigating the realistic sintering process in the porous structure of the Ni/YSZ anode and for designing durable anode structures for SOFCs.