© 2019 American Physical Society. The mixed quantum-classical nonadiabatic molecular dynamics (NAMD) is a powerful tool to study many phenomena, especially ultrafast carrier transport and cooling. Carrier decoherence and detailed balance are two major issues in NAMD. So far, there is no computationally inexpensive approach to incorporate both effects. While the decoherence effect can be easily included in the state density matrix formalism and the detailed balance can be included in surface hopping or the wave function collapse approach, it is difficult to include both of them in a unified formalism. In this work we introduce a state density matrix formalism (referred to as P-matrix) including both the decoherence and detailed balance effects for NAMD. This method is able to explicitly treat the decoherence between different pairs of adiabatic states. Moreover, the off-diagonal density matrix elements are divided into two parts, corresponding to energy-increasing and energy-decreasing transitions. The detailed balance is then enforced by a Boltzmann factor applied to the energy-increasing transition part. The P-matrix formalism is applied to study hot-hole cooling and transfer processes in Si quantum dot (QD) systems. The calculated hot-carrier relaxation time is consistent with experiments. In a QD-pair system, the hot-hole cooling time shows weak dependence on the QD spacing. However, the hot-carrier transfer rate from one QD to another is found to decrease exponentially with the QD-QD distance. When the QD spacing is small (∼1 nm), the hot-carrier transfer can be very efficient. It is also shown that the explicit treatment of decoherence time is important in order to treat this hot-carrier transfer correctly.