In order to solve the problem that there exists the photothermal effect during the trapping by a metal optical nanotweezer structure, an optical tweezer structure with silicon-based double nanoballs is designed. The three-dimensional finite element method in frequency domain is used to compare and analyze the enhanced field distributions as well as the thermal effects under the same trapping potential energy of polystyrene nanoparticles for the structures with silicon-based double nanoballs and with gold-based double nanoballs. It is found that the silicon-based structure has a relatively low thermal effect and good trapping stability under a high light field intensity. The trapping of polystyrene nanoparticles by the designed silicon-based double nanoballs is simulated, and the trapping forces under a stable field at different positions of nanoparticles with different diameters are studied. The research results show that the silicon-based optical nanotweezer structure can trap nanoparticles stably and simultaneously suppress the structural thermal effects efficiently.