Functional nanomaterials possess exceptional mechanical, electrical, and optical properties which have significantly benefited their diverse applications to a variety of scientific and engineering problems. In order to fully understand their characteristics and further guide their synthesis and device application, the multiphysical properties of these nanomaterials need to be characterized accurately and efficiently. Among various experimental tools for nanomaterial characterization, scanning electron microscopy- (SEM-) based platforms provide merits of high imaging resolution, accuracy and stability, well-controlled testing conditions, and the compatibility with other high-resolution material characterization techniques (e.g., atomic force microscopy), thus, various SEM-enabled techniques have been well developed for characterizing the multiphysical properties of nanomaterials. In this review, we summarize existing SEM-based platforms for nanomaterial multiphysical (mechanical, electrical, and electromechanical) in situ characterization, outline critical experimental challenges for nanomaterial optical characterization in SEM, and discuss potential demands of the SEM-based platforms to characterizing multiphysical properties of the nanomaterials.