The asymmetric dark matter (ADM) scenario can solve the coincidence problem between the baryon and the dark matter (DM) abundance when the DM mass is of ${cal O}(1),$GeV. In the ADM scenarios, composite dark matter is particularly motivated, as it can naturally provide the DM mass in the ${cal O}(1),$GeV range and a large annihilation cross section simultaneously. In this paper, we discuss the indirect detection constraints on the composite ADM model. The portal operators connecting the $B-L$ asymmetries in the dark and the Standard Model(SM) sectors are assumed to be generated in association with the seesaw mechanism. In this model, composite dark matter inevitably obtains a tiny Majorana mass which induces a pair-annihilation of ADM at late times. We show that the model can be efficiently tested by the searches for the $gamma$-ray from the dwarf spheroidal galaxies and the interstellar electron/positron flux.