Abstract: With the continuous advances in geotechnical engineering practice, especially in deep-underground, deep-sea and deep-space areas (engineering of three-deep-area), geo-engineers are faced with increasingly complex geomaterials and geotechnical environment. Based on the continuum mechanics and phenomenological methodologies, the conventional soil mechanics encounters many difficulties in describing the complicated behavior of soils, such as discontinuous response, large deformation and failure, and the impacts of complex environment. Geomechanics from micro to macro (GM3) starts from particle-scale characterization of soils and upscales to its macroscopic behavior. In this way, the microscopic mechanisms can be revealed to understand the complex behavior of problematic soils. Then the multi-scale theories and methodologies established can promisingly solve the key problems in geomechanics and geotechnical engineering and finally upgrade engineering design level. This paper first highlights the main development of GM3 in the past 40 years. The methodologies, theories, applications of GM3 developed by the worldwide researchers are then introduced, including microscopic behavior of typical soils, microscopic constitutive models, micro-macro bridging and macroscopic constitutive models based on the micro-mechanisms. Various soils are discussed, including clays, structured sands and loesses on the earth, deep-sea methane hydrate bearing sediments, and planetary soils (lunar regolith). The focus is put on the applications and extensions of distinct element method (DEM) in the simulations of problematic geomaterial mechanics and geotechnical engineering on and off shore and in the deep-space. Finally, serveral key challenges and opportunities in GM3 are discussed. By systematically reviewing the above achievements, the paper outlines GM3 framework in order to accelerate the development of research in this area.