Magnetic field plays a very important role in many astronomical phenomena at various scales of the universe. It is no exception in the early universe. Since the energy density, pressure, and tension of the primordial magnetic field affect gravitational collapses of plasma, the formation of seeds for large scale structures should be influenced by them. Here we numerically investigate the effects of stochastic primordial magnetic field on the seeds of large scale structures in the universe in detail. We found that the amplitude ratio between the density spectra with and without PMF (|P (k)/P0(k)| at k > 0.2 Mpc −1 ) lies between 75% and 130% at present for the range of PMF strengths 0.5 nG < B λ < 1.0 nG, depending on the spectral index of PMF and the correlation between the matter density and the PMF distributions.