The SST (Space Solar Telescope) is an astronomical telescope with a primary mirror of 1 m in diameter. It observes the sun with a small view field to ensure that its high spatial resolution imaging has 0.1″-0.15″ and high SNR (signal to noise ratio). Surrounding the small view field is still the sun, which is an intense source of both heat and stray light. The baffles (the main baffle, the aperture, and the outer baffle), which are used to eliminate the stray light, will change the thermal flux in the SST and will weaken the effect of the thermal control design. In this study, the compatibility analysis of the thermal effect of baffle structures in SST is performed. The GCF (Geometry Composing Function) and BRDF (Bidirectional Reflectance Distribution Function), which are two inherent related parameters in the compatibility analysis, are derived. The objective and method of the compatibility analysis are determined. With the thermal analysis software, the temperature fields are calculated for different lengths of the main baffle, different radii of apertures, different lengths of the outer baffle with a 3′ tilt angle and 16′ tilt angle, and different tilt angles of the outer baffle with a 200 mm length. A series of configurations and sizes of the baffles are studied with the goals of both thermal control and elimination of stray light. The design of the baffle structure of SST is achieved: the main baffle of length 4100 mm, the internal shield of radius 494 mm, the outer baffle of length 200 mm, and the outer baffle of tilt angle 3′ are successfully designed. This paper presents the relationship between the thermal control design and stray light elimination plan in the SST. The aims of the optimal design of the baffle structure of SST are reached. The thoughts and methods of the optimal analysis are also useful for similar optical telescopes designed for solar observation.