This paper reports a synthetic route to CuInSe2 (CISe) ternary 3D and 1D nanostructures with a controlled shape by combining a oriented attachment and ligand protection strategy. A mixture of trioctylphosphine oxide (TOPO), trioctylphosphine (TOP) and aliphatic amine used as both a capping agent and a reaction solvent was found to be very suitable for the preparation of three-dimensional flower-like, branched multipod nanostructures, and one-dimensional nanowires, under various growth conditions. TOPO/TOP were found to retard the nucleation process, and amine could be used as an activation agent by coordinating it with precursors to assist with fast nucleation. By taking advantage of these two mechanisms (retarding and activating reaction), the rate of the nucleation process could be regulated and CISe nanoflowers could be obtained. Comparison of various experiments show that several experimental parameters, such as reaction temperature, time, and several capping ligands (primary, secondary, and tertiary amines) play important roles in the control of the morphology and size of CISe nanostructures. Detailed structure and composition characterizations are presented, employing scanning electron microscopy, energy-dispersive X-ray spectrometry, transmission electron microscopy, and X-ray diffraction.