We investigate the dynamics of photonic crystal (PC) molecules with Kerr nonlinearity by numerical simulations in a pump-probe scheme based on the finite-difference time-domain technique. The constitutional PC atoms of the nonlinear PC molecules are intentionally chosen to be multimode so that the pump and probe waves can be set at different frequencies, ensuring the clear identification of the dynamics of nonlinear PC molecules. Being more complicated than the dynamics of nonlinear PC atoms, we reveal that the coupling between the PC atoms plays an important role in determining the dynamical responses of nonlinear PC molecules to the excitation of ultrashort pulses. It is reflected in fact that PC molecules with different spectral shapes exhibit different dynamical response behaviors.