The rise of global shale oil and gas exploration has prompted scholars to pay attention to the mechanics of organic matter (OM) in shale reservoirs. The depth-sensing nanoindentation, a rather mature micromechanical testing technique in materials science, was gradually introduced into the mechanical data acquisition of shale matrix OM in recent years. Although this introduction is commendable, there are still some attentive issues relating to the indentation condition (mainly the reasonable setting of indentation depth parameter) and interpretation of the measured mechanical data, considering the micron-sized and nanoporous nature of OM and its close contact with surrounding minerals in shale composite. This study carried out a series of OM-positioned indentations on a typical shale sample collected from Silurian Longmaxi Formation in South China, in which we specially used the dynamic mechanical analysis that determines the mechanical data as a continuous function of indentation depth. Through it, we evidenced two main indentation effects (i.e., the size and substrate) during indentation of OM, and quantified the depths they appear (at less than 200 nm and greater than 1/20 of OM thickness, respectively). They together limit the indentation depth to a narrow range and also restrict the use of nanoindentation for OM less than 2 μm. Additionally, the porous OM is measured to be in lower mechanical values, suggesting that the porous effect on the indentation response cannot be ignored, especially when making mechanical comparison between different OM particles. Furthermore, we compared nanoindentation with the newly developed AFM-based nanomechanical mapping technique, and proposed to combine the both to achieve a full-scale characterization of shale matrix OM. Overall, this study standardized the indentation conditions to measure the inherent mechanical data of shale matrix OM, which lays the foundation for the forseeable increasing demand for testing and research of OM mechanics in the future.