We present the thermal model of the Balloon-borne Large-Aperture Submillimeter Telescope for Polarimetry (BLASTPol). This instrument was successfully own in two circumpolar flights from McMurdo, Antarctica in 2010 and 2012. During these two flights, BLASTPol obtained unprecedented information about the magnetic field in molecular clouds through the measurement of the polarized thermal emission of interstellar dust grains. The thermal design of the experiment addresses the stability and control of the payload necessary for this kind of measurement. We describe the thermal modeling of the payload including the sun-shielding strategy. We present the in-flight thermal performance of the instrument and compare the predictions of the model with the temperatures registered during the flight. We describe the difficulties of modeling the thermal behavior of the balloon-borne platform and establish landmarks that can be used in the design of future balloon-borne instruments.