Rail welded joints are integral part of continuous welded rail. However, they often do not have sufficient reliability during the operation. The article is devoted to the assessment of temperature influence effect on the mechanical properties and structure of weld metal and welded rails. The temperature distribution across the rail section in welded zone during the cooling process of aluminothermic rail welding is obtained using simulation by LVMFlow. The results of the study of hardness and structure of metal rail aluminotermitic welded joints are given. It is shown that the hardness of rail welded joints increases from 24 HRC to 38 HRC in the fusion zone of the weld metal and rail metal. It is due to the harmful effects of overheating of the metal during the welding process. The hardness is confirmed by microstructural analysis. Microstructural analysis showed the differences in the grains sizes of metal welded zone and heat affected zone. The structure of welded metal is acicular dendritic. Owing to a difference between structures of the welded joint zones the probability of occurrence of cracks on the boundary of fusion weld and metal is increased.