The disclosure discloses a method and device for controlling a composite scanning device, and a composite scanning system. The composite scanning system includes: a composite scanning device and a host which includes: an application module configured for performing a first capability setting on the composite scanning device, obtaining the scanned image data from the composite scanning device after the first capability setting, and processing the scanned image data in a first TWAIN session state; and a configuration module configured for performing a second capability setting on the composite scanning device according to the processing result of the application module in the first TWAIN session state. By the disclosure, the efficiency of capability setting in the composite scanning system which is compatible with TWAIN protocol can be improved.