In this work, we propose a secret key generation procedure specifically designed for the inter-spacecraft communication links. As a novel secrecy source, the spacecrafts utilize Doppler frequency shift based measurements. In this way, the mobilities of the communication devices are exploited to generate secret keys, where this resource can be utilized in the environments that the channel fading based key generation methods are not available. The mobility of a spacecraft is modeled as the superposition of a pre-determined component and a dynamic component. We derive the maximum achievable secret key generation rate from the Doppler frequency shift. The proposed secret key generation procedure extracts the Doppler frequency shift in the form of nominal power spectral density samples (NPSDS). We propose a maximum-likelihood (ML) estimation for the NPSDS at the spacecrafts, then a uniform quantizer is utilized to obtain secret key bits. The key disagreement rate (KDR) is analytically obtained for the proposed key generation procedure. Through numerical studies, the tightness of the provided approximations is 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.