The $J/psi$-nucleon interaction is studied by lattice QCD calculations. At the leading order of the derivative expansion, the interaction consists of four terms: the central, the spin-spin, and two types of tensor forces. We determine these spin-dependent forces quantitatively by using the time-dependent HAL QCD method. We find that the spin-spin force is the main cause of the hyperfine splitting between the $J=1/2$ and the $J=3/2$ states, while the two tensor forces have much smaller effects on the S-wave scattering processes.