Al alloy and Mg alloy are not only the lightest metal structural materials, but also have the advantages of high specific strength and damping performance, which are very attractive for automobile, high-speed rail and aerospace. To meet the requirements of structural lightweight and different service environments, it is usually necessary to join Al alloy and Mg alloy into a complete structure. As a new solid-state joining method, friction stir welding (FSW) has obvious advantages in the field of Al alloy/Mg alloy hybrid structure because its welding temperature is lower than the melting point of base metal. However, the formation temperature of Al alloy/Mg alloy intermetallic compounds (IMCs) is lower than the melting point of Al and Mg, if the thickness of base metal exceeds 10 mm, the Al alloy/Mg alloy FSW is still very difficult because of the formation of IMCs in the weld. To obtain some control methods of the formation of IMCs, 5A06-H112 Al alloy and AZ31B-O Mg alloy plates with a thickness of 15 mm were used for the Al alloy/Mg alloy FSW. Liquid nitrogen was sprayed near the rear of the stirring head to locally cool the upper surface of the weld. EBSD and TEM instrument were used to obtain the phase distribution and grain orientation spread at different positions of the welded joint. The precipitation behavior of IMCs at the interfaces on both sides of the stirring zone (SZ) of Al alloy/Mg alloy joints under ambient temperatures and liquid nitrogen cooling conditions was studied. The results indicate that Al₃Mg₂ mainly precipitates on the Al alloy side of SZ; the main precipitation on the Mg alloy side is Al₁₂Mg₁₇, and it was generated eutectic reactions with Mg at the upper interface; liquid nitrogen cooling on the surface can reduce the peak temperature and high-temperature residence time at various positions of the joint, and has a significant inhibitory effect on the precipitation of IMCs and the formation of low melting point eutectic. When surface cooling is not applied, almost only Al₃Mg₂ phase is precipitated in the SZ at the upper and middle parts of near the interface of Al alloy side, and at the bottom, only fine equiaxed Al grains are observed in the SZ. At the side of magnesium alloy, Al₁₂Mg₁₇ phase is mainly precipitated at the upper interface of SZ and it forms low melting point eutectic with Mg, and at the same time, a thin layer of Al₃Mg₂ is precipitated between the eutectic zone and the Al alloy in SZ. Two layers of Al₃Mg₂ and Al₁₂Mg₁₇, which are sticked close to each other and there is a distinct boundary layer between them, is precipitated between SZ and the Mg alloy at the middle and lower interfaces, and the total thickness of the IMCs layer at the middle interface is much greater than the IMCs layer thickness at the bottom interface, at here the peak temperature is lower, the thickness of the Al₃Mg₂ layer is decreased more significantly. When liquid nitrogen cooling is applied to the weld surface, in addition to Al₃Mg₂ phase precipitation, there are also a small number of Al₁₂Mg₁₇ and Al grains in the SZ at the upper part of the interface of Al alloy side, while equiaxed Al grains are present in the SZ at the middle and bottom parts of the interface. At interface close to the Mg alloy side, the precipitation behavior of IMCs in each parts is similar to that without surface cooling, but the total thickness of the Mg + Al₁₂Mg₁₇ eutectic layer and Al₃Mg₂ layer precipitated at the upper part of the interface, and the thickness of the IMCs layer at the middle and lower SZ interfaces are significantly decreased, and the thickness of the Al₃Mg₂ thin layer decreases more significantly. The strain rate has a significant impact on the precipitation of IMCs, and it is confirmed by that, the actual thickness of the interface layer is much greater than the theoretical thickness calculated by the diffusion law.