We investigate the coupling of photonic crystal (PC) defects by using coupled-mode theory. The PC molecules formed by the coupling of two identical PC atoms are the focus of our study. It is revealed that the flatness of the transmission spectra of the PC molecules is determined uniquely by the phase shift of the travelling wave between the two coupled PC atoms. By properly adjusting the distance between the two constitutional PC atoms, we are able to modify the transmission spectrum of the resulting PC molecule. Theoretical analyses based on the coupled-mode theory are in good agreement with the simulation results obtained by the transfer matrix method and the finite-difference time-domain technique.