Structural fluctuation in a Pd 40Ni 40P 20 bulk metallic glass is investigated by transmission electron microscopy and electron diffraction. Local atomic ordered regions with a fcc-(Pd,Ni) type structure was sharply imaged by a high-resolution electron microscopy (HREM) attached with a Cs-corrector. Interference function for the glassy state was obtained from electron-diffraction intensity profiles using energy-filter and imaging-plate techniques. We used a reverse Monte Carlo (RMC) simulation method to develop a realistic structure model. The model consists of a dense-random-packing structure, in which an fcc ordered region with Pd, Ni, and P atoms was embedded. The structure model is consistent with the diffraction and HREM results. In Voronoi polyhedral analysis of the RMC simulated structure, P-centered (Pd,Ni)-P trigonal prisms are found primarily in the matrix structure embedding the fcc-cluster. Around Pd and Ni atoms deformed-fcc type polyhedra were frequently observed. From these local structural features, nanoscale phase separation was revealed to occur during the glass formation.