The discovery of two-dimensional (2D) materials with single or a few-atom-thick layers has presented unprecedented opportunities to study, control and harness the properties of van der Waals (vdW) materials at their 2D limit. It also offers a platform that allows the arbitrary creation of heterostructures in a materials-by-design approach with properties tailored by the constituting components. Combining organic molecules with 2D materials to form hybrid heterointerfaces has recently emerged as a facile and versatile approach to engineer the electronic, optical, magnetic and chemical properties of 2D materials for new or optimized device applications. Underpinning the development of organic–2D materials heterostructures is the ability to interrogate the interfacial electronic structures and properties at multiple dimensions. This review provides a timely update on the application of synchrotron-based soft X-ray spectroscopies (SR-SXS) in the characterization of organic–2D materials interfaces. By harnessing the unparalleled high energy resolution, tunable energy, high brilliance and tunable polarization inherent to synchrotron radiation, electronic structures, charge transfer dynamics, molecular orientations and spin configurations at the hybrid interfaces can be examined, which helps us to formularize a coherent understanding of the organic–2D materials interfaces that will guide the design of new hybrid vdW structures and devices. We also offer our perspective on the future application of SR-SXS in the exploration of organic–2D materials heterostructures.