An instrumental system and the corresponding experimental technique for multiparametric nanoscale 3D characterization of a wide range of composite nanomaterials have been developed. This system makes it possible to obtain 3D data on the chemical composition of a material by optical methods in the confocal and near-field optical microspectroscopy modes (fluorescence and Raman) with a lateral resolution up to 50 nm, as well as data on the 3D morphology and spatial distribution of mechanical, electrical, and other characteristics of the material in the scanning probe microscopy mode with a resolution of about 10 nm on the X and Y axes and several angstroms on the Z axis, for a single area of the sample (100 μm × 100 μm × 3 mm). The nanoscale 3D pattern of the distribution of these characteristics is obtained by sequentially examining nanomaterial layers at a step of 20 nm along the Z axis and a total depth of Z-scanning of 3 mm.