A new non-Markovian stochastic Schrödinger equation at finite temperatures is presented to correctly describe charge carrier dynamics in organic molecular crystals. The electron-phonon interactions in both site energies and electronic couplings are incorporated by the time-dependent complex-valued random fluctuations which are generated from corresponding spectral density functions. The approach is thus easily extended to investigate coherent-to-hopping charge transfer in systems with thousands of molecular sites. The capability of present approach is demonstrated by numerical simulations of carrier dynamics in the spin-boson model and a realistic Fenna-Matthews-Olson complex. The results manifest that the non-Markovian effect and complex-valued random forces are essential to guarantee the detailed balance. In an application to a long-chain donor-acceptor system, it is also interesting to find a property of coherent-to-hopping charge transfer from temperature dependence of diffusion coefficients.