The shape controlled synthesis of high quality colloidal lead selenide (PbSe) nanocrystals (NCs) was achieved through a simple solvothermal process. By using oleic acid (OA) as a ligand and activating agent for the Pb precursor, the evolution of the NCs from nanospheres to nanoflowers and finally to nanocubes was achieved by increasing the reaction time. Further, the shape variation from nanospheres to polyhedrons was readily realized through the increase of OA concentration in the stock solution. More interestingly, the change of the anion ligand was proven to be a facile method to control the structure and size of the nanoflowers. The X-ray diffraction and TEM analysis demonstrated the cubic rock salt structure of the synthesized PbSe NCs. Accompanied by comprehensive analytics, the discussion on the possible mechanisms for the shape evolution was provided.