Abstract The crystal phases are essential to the physicochemical properties and functionalities of materials. Copper selenide has emerged as an important and appealing semiconductor, which can exist in a variety of polymorphic phases. However, the richness of polymorphs also makes it a challenge to the direct preparation of copper selenide nanocrystals with tunable phases. Herein, two polymorphs, that is, quasi‐tetragonal Cu2−xSe nanocubes and metastable wurtzite Cu2Se nanodisks, are successfully synthesized by using a single precursor, copper(I) selenocyanate (CuSeCN), as the Cu and Se sources. The key to phase modulation is the optimal choice of the ligand in the synthesis. The as‐prepared nanocrystals possess different morphologies and compositions, giving rise to distinct optical properties and electrical conductivities. Interestingly, the copper selenide nanocrystals can provide a platform for the rational construction of two types of amorphous hollow Au─Cu─Se nanostructures by reaction with Au(I) precursor, in which their final shapes are well kept as that of the original nanocrystal templates. This work provides an easy strategy for the phase‐controlled synthesis of copper selenide nanocrystals and enables the design of new materials for broad applications.