Infrared imaging is widely applied in the discrimination of spatial targets. Extracting distinguishable features from the infrared signature of spatial targets is an important premise for this task. When a target in outer space experiences micro-motion, it causes periodic fluctuations in the observed infrared radiation intensity signature. Periodic fluctuations can reflect some potential factors of the received data, such as structure, dynamics, etc., and provide possible ways to analyze the signature. The purpose of this paper is to estimate the micro-motion dynamics and geometry parameters from the observed infrared radiation intensity signature. To this end, we have studied the signal model of the infrared radiation intensity signature, conducted the geometry and micro-motion models of the target, and we proposed a joint parameter estimation method based on optimization techniques. After analyzing the estimation results, we testified that the parameters of micro-motion and geometrical shape of the spatial target can be effectively estimated by our estimation method.