The evolution of precipitate orientation and its effect on the thermal conductivity of Mg-5Sn alloys under different treatments were systematically investigated. The results show that for the alloy subjected to aging prior to twinning (Sample AT), the basal precipitates are precisely regulated to be the prismatic precipitates, and the lath-shaped precipitates experience a rigid rotation of 3.7° to accommodate the twinning shear. For hexagon-shaped precipitates with a larger thickness in Sample AT, the precipitate only experiences a small rigid rotation of 0.2°, due to the development of stacking faults releasing part of the strain at the precipitate/twin interface. In addition, the orientation of precipitates has a significant effect on the thermal conductivity of the alloy. When the measurement direction of thermal conductivity is parallel to extrusion direction (ED), the precipitates lying on the basal plane, perpendicular to ED, are more beneficial to the improvement of thermal conductivity than precipitates lying on the prismatic plane parallel to ED. Sample TA (aging after twinning) with precipitates lying on the basal plane shows the best thermal conductivity of 137.81 W/(m×K).