Three-dimensional seed phenotyping requires imaging systems capable of achieving micron-level resolution across a centimeter-level field of view (FOV), a goal constrained by the resolution–FOV trade-off in conventional light field architectures. This paper presents a hardware–software co-optimized framework that integrates a reconfigurable optical system with computational imaging pipelines to address this limitation. At the hardware level, we develop a tunable-focus lens module that enables flexible adjustment of the effective focal length, combined with a custom-designed microlens array (MLA). A mathematical model is established to analyze the interdependencies among FOV, lateral resolution, depth of field (DOF), and system configuration, guiding the design of individual optical components. On the computational side, we propose a hybrid aberration correction strategy: first, a co-calibration of lens and MLA aberrations based on line-feature detection; second, a conditional generative adversarial network (cGAN) with attention-guided residual learning to enhance sub-aperture images, achieving a PSNR of 34.63 dB and an SSIM of 0.9570 on seed datasets. Experimentally, the system achieves a resolution of 6.2 lp/mm at MTF50 over a 2–3 cm FOV, representing a 307% improvement over the initial configuration (1.52 lp/mm). The reconstruction pipeline combines epipolar plane image (EPI) analysis with multi-view consistency constraints to generate dense 3D point clouds at a density of approximately 1.5 × 10⁴ points/cm² while preserving spectral and textural features. Validation on bitter melon and rice seeds demonstrates accurate 3D reconstruction and accurate extraction of morphological parameters across a large area. By integrating optical and computational design, this work establishes a reconfigurable imaging framework that overcomes the resolution–FOV limitations of conventional light field systems. The proposed architecture is also applicable to robotic vision and biomedical imaging.