We propose a novel physical layer secret key generation method for the inter-spacecraft communication links. By exploiting the Doppler frequency shifts of the reciprocal spacecraft links as a unique secrecy source, spacecrafts aim to obtain identical secret keys from their individual observations. We obtain theoretical expressions for the key disagreement rate (KDR). Using generalized Gauss-Laguerre quadrature, we derive closed form expressions for the KDR. Through numerical studies, the tightness of the provided approximations are shown. Both the theoretical and numerical results demonstrate the validity and the practicality of the presented physical layer key generation procedure considering the security of the communication links of spacecrafts.