A transparent display system, a control method and a control device thereof are provided. The transparent display system includes an information capturing assembly, a transparent display and a control device. The information capturing assembly is used to obtain at least one detection content. The control device includes a detection unit, a resource allocation unit and a recognition unit. The detection unit is used for detecting at least one user in front of a transparent display and at least one target object behind the transparent display according to the detection content. The resource allocation unit is used to obtain a resource allocation according to a detection result of the detection content. The information capturing assembly obtains at least one recognition content. The recognition unit obtains at least one front side position of the user and at least one back side position of the target object according to the resource allocation.