The influence of thermal blooming effect on the flat-topped laser beam array propagating through the atmosphere is studied, where coherent beam combination and incoherent beam combination are considered. The results show that the beam spot of flat-topped laser beam array propagating through the atmosphere with cross wind is like a crescent pattern. For coherent beam combination, multiply intensity peaks exist in the beam spot. For incoherent beam combination, there is always one intensity peak. The flat-topped laser beam array for incoherent beam combination is less affected by the thermal blooming than that for coherent beam combination. The flat-topped laser beam array with larger beam order N is less affected by the thermal blooming than that with smaller one. Hence, comparing with the flat-topped laser beam array, the thermal blooming is more serious for the Gaussian beam array (N=1). With the increase of N, the propagation efficiency decreases in free space, but it increases in the atmosphere. Under the condition of the same beam power in atmosphere, the propagation efficiency of flat-topped laser beam array is better than that of Gaussian laser beam array.