Understanding of the sintering mechanism of nickel nanoparticles in the Ni/YSZ anode is requested for long-term durability of solid oxide fuel cell. To elucidate the effects of a porous structure of the Ni/YSZ anode on the sintering, we investigated the sintering process in the Ni/YSZ anodes with different porosities by using our developed multi-nanoparticle molecular dynamics simulation method. We found that the nickel nanoparticle size significantly increased although the YSZ nanoparticles showed little change during the sintering in all the Ni/YSZ models. Since the decrease in the porosity leads to the decrease in the pore size of the YSZ framework, the sintering of the nickel nanoparticles in the Ni/YSZ model with the less porosity is more prevented by suppressing the neck growth in the small pore. On the other hand, the excessively large porosity increases the distance between the nickel nanoparticles and prevents the nickel nanoparticles from contacting.