The present invention discloses a three-dimensional in-situ characterization method for heterogeneity in generating and reserving performances of shale. The method includes the following steps: establishing a logging in-situ interpretation model of generating and reserving parameters based on lithofacies-lithofacies-well coupling, and completing single-well interpretation; establishing a 3D seismic in-situ interpretation model of generating and reserving parameters by using well-seismic coupling; establishing a spatial in-situ framework of a layer group based on lithofacies-well-seismic coupling, and establishing a spatial distribution trend framework of small layers of a shale formation by using 3D visualized comparison of a vertical well; and implementing 3D in-situ accurate characterization of shale generating and reserving performance parameters by using lithofacies-well-seismic coupling based on the establishment of the seismic-lithofacies dual-control parameter field. The present invention integrates an in-situ technology into shale logging, seismic generating and reserving parameter interpretation, and the establishment of a 3D mesh model of small layers of shale, which realizes the accurate description of the heterogeneity in TOC content and porosity value of shale oil and gas in a 3D space, and provides a reliable technical support for shale oil and gas exploration and development.