The quantum-confined stark effect induced by polarization has significant effects on the optical properties of nitride heterostructures. In order to improve the emission efficiency of GaN/AlN quantum dots [QDs], a novel epitaxial structure is proposed: a partially relaxed GaN layer followed by an AlN spacer layer is inserted before the growth of GaN QDs. GaN/AlN QD samples with the proposed structure are grown by molecular beam epitaxy. The results show that by choosing a proper AlN spacer thickness to control the strain in GaN QDs, the internal quantum efficiencies have been improved from 30.7% to 66.5% and from 5.8% to 13.5% for QDs emitting violet and green lights, respectively.