To date, our understanding concerning materials in the deep lithosphere relies primarily on two ways: ① a geophysics- based methodology (in which geophysical features of deep components are speculated according to those of exposed rock); ② a xenolith- based methodology. In this study, we explore the third way, a methodology that employs rock probe and multi- proxy isotopic mapping as the core. Combined with synthetical petrographic and petrogenetic studies on magmatic rocks derived from multiple sources at different depths, rock probe and multi- proxy isotopic mapping can be a suite of valuable tools in deciphering the 3- D lithospheric material architecture and its 4- D evolutionary history. Based on this, we attempt to incorporate the three methodologies into a novel methodological system for exploring the lithospheric material architecture. This will shed new light on the detection of the deep lithosphere. Previous studies have revealed that, based on petrographic observations, isotopic mapping by integrating Sr, Nd, Hf, Pb and other isotopes, combined with geophysical results, is capable of unraveling the material architecture of the deep lithosphere. These advances demonstrate the consistency and effectiveness of multi- proxy isotopic systems in tracing deep materials and the correspondence between the isotopic mapping and geophysical detection results. Therefore, we propose a methodological framework for deciphering the 3- D material architecture of the lithosphere. The application of this methodology in the Central Asian Orogenic Belt (accretionary orogen), Tibet Plateau (collisional orogen), and the North China and Yangtze cratons has yielded some encouraging advances, indicating the significant application potential of this methodology. The achievements documented in this paper suggest that a novel methodological system has been prepared for deciphering the deep lithospheric materials and elucidating the architectures of crust and mantle.