Seed phenomics is a critical research field for understanding seed germination mechanisms. Metasurfaces, composed of subwavelength nanostructures, offer a promising pathway to achieve both dispersion control and imaging functionalities within an ultra-compact form factor. Recent advances in micro–nano-optics and computational imaging have opened new avenues for high-dimensional, multimodal imaging. However, conventional hyperspectral and light-field systems still face limitations in compactness, depth resolution, and spectral–spatial integration. This review summarizes recent progress in metalens and metasurface lens array-based light-field systems for hyperspectral imaging and 3D reconstruction, with a focus on the underlying principles, design strategies, and reconstruction algorithms that enable single-shot 3D hyperspectral acquisition. We further present a forward-looking roadmap toward the realization of a revolutionized imaging paradigm: a metasurface-based light-field platform that fully integrates 3D and hyperspectral imaging capabilities. In particular, we examine how dispersive metasurfaces serve as core optical elements for precise dispersion control in hyperspectral imaging systems, while metalens arrays enable accurate modulation of spatial–angular distributions in light-field configurations. We systematically review both 3D and spectral reconstruction algorithms, highlighting their roles in decoding complex optical encodings. The application of these integrated systems in seed phenotyping is emphasized, demonstrating their capability to capture 3D spatial–spectral distributions in a single exposure. This approach facilitates high-throughput analysis of morphological traits, germination potential, and internal biochemical composition, offering a comprehensive solution for advanced seed characterization. Finally, we outline a practical roadmap for implementing a metasurface-based light-field platform that integrates hyperspectral imaging and computational 3D reconstruction. This review offers a comprehensive overview of the state of the art in compact 3D light-field systems and multimodal hyperspectral imaging platforms, while providing forward-looking insights aimed at advancing smart seed phenotyping, precision agriculture, and next-generation optical imaging technologies.