Binary nickel–cobalt oxy-hydroxides (denoted as NCOH) with tunable crystal phases are prepared from an atomic mixture of Ni(OH)2 + Co(OH)2 in the 1:2 ratio (denoted as (Ni/2Co)(OH)2) through a microwave-assisted hydrothermal annealing (MAHA) method. The (Ni/2Co)(OH)2 powders are synthesized through a sol–gel process from an aqueous solution containing NiCl2·6H2O and CoCl2·6H2O. The MAHA process is demonstrated to be a novel and promising method for transforming/tuning the crystal phase and size of NCOH at relatively low annealing temperatures in short time. The MAHA temperature and time are varied to transform the crystalline phases from a hydroxide mixture to NiCo2O4 nanocrystals, which can be quantified by a crystalline index (denoted as CI) value obtained from X-ray diffraction (XRD) patterns. The higher content and larger size of NiCo2O4 nanocrystals are, the longer electrochemical activation time is needed. The rate of phase transformation can be enhanced by adding microwave adsorbents, graphene oxide (GO), to obtain a NiCo2O4/RGO composite with reduced crystal size (RGO: reduced GO). The variation in the crystalline index and the effect of the potential window on the specific capacitance of NCOH powders are systematically compared and discussed in this work.