A system and associated method for compensating for thermal deformation of a spaced-based structure having a spacecraft payload. The system including a beacon source coupled to a first spacecraft for transmitting a first signal and a beacon sensor coupled to a second spacecraft for receiving the first signal and providing measurement data derived from the first signal. At least one attitude sensing device is coupled to the second spacecraft for determining estimated spacecraft attitude data for the second spacecraft. A processor on the second spacecraft is configured to process ephemeris data of the first and second spacecraft, beacon measurement data, estimated spacecraft attitude data, and gimbal angular position data to estimate spacecraft structural deformation.