We construct a leading-order effective field theory for both scalar and axial-vector heavy diquarks, and consider its power expansion in the heavy diquark limit. By assuming the transition from QCD to diquark effective theory, we derive the most general form for the effective diquark transition currents based on the heavy diquark symmetry. The short-distance coefficients between QCD and heavy diquark effective field theory are also obtained by a tree level matching. With the effective currents in the heavy diquark limit, we perform a reduction of the form factors for semi-leptonic decays of doubly heavy baryons, and find that only one nonperturbative function is remaining. It is shown that this soft function can be related to the Isgur-Wise function in heavy meson transitions. As a phenomenological application, we take a single pole structure for the reduced form factor, and use it to calculate the semi-leptonic decay widths of doubly heavy baryons. The obtained results are consistent with others given in the literature, and can be tested in the future.