Embodiments of this application provide a heat exchanger, a modular indirect evaporation cooling system, and a method for controlling a modular indirect evaporation cooling system, and relate to the field of indirect cooling technologies, to improve cooling efficiency of the modular indirect evaporation cooling system. The heat exchanger includes a first heat exchange core and a second heat exchange core. The first heat exchange core includes a first heat exchange fin and a first seal, where two first seals are disposed opposite to each other and are separately connected to the first heat exchange fin in an intersected manner. The second heat exchange core includes a second heat exchange fin, a second seal, and a heat exchange medium permeability channel, where two second seals are opposite to each other and are separately connected to the second heat exchange fin in an intersected manner.