The polygenic and polychronous character of zircon texture is the key source of information on the conditions of its growth and secondary alterations. In this research the JPD method of processing of the BSE and CL images including plotting of JPD histograms and JPD maps of grains was developed and applied for quantitative study of the internal texture of zircon grains with micron spatial resolution and for its use in geochronometry. The nomenclature for distinguished zones on the generalized diagram (BSE vs. CL) is suggested for zircons of a wide range of the conditions of its formation, age, size, texture types, and degrees of structure disordering. The JPD-analysis of zircon internal texture is applied for interpretation of the nature of variations in the BSE and CL intensities within an individual heterogeneous grain (on the quantitative level) and between different grains (on the qualitative level). The approach is suggested as the preliminary stage during geochronological studies increasing the reliability of the local electron microprobe and mass spectrometry isotope dating of the mineral.