Geotechnical engineering challenges, such as bouldery debris flows and landslide-structure impacts, inherently involve complex, three-dimensional (3D) large-deformation interactions among granular soil, water, rocks, and flexible structures. Modelling these dynamic multiphase systems poses significant difficulties for traditional grid-based methods due to severe mesh distortion and intricate spatial topological changes. Addressing these challenges, this study presents a unified, fully 3D Lagrangian Smoothed Particle Hydrodynamics (SPH) framework tailored for computational geomechanics. The proposed framework is built upon four key features: (1) Large deformation handling: Utilizing a mesh-free Lagrangian approach to naturally capture violent free-surface flows and large soil distortions; (2) Unified multi-phase formulation: A rigorous coupling strategy is employed where soil and water are modelled using a Riemann-based Updated Lagrangian SPH, while rocks and flexible structures are discretized via Total Lagrangian SPH. The soil-water interaction is resolved using a robust two-layer formulation; (3) Multi-physics integration: The solver consistently integrates fluid dynamics, elastoplastic soil mechanics, and solid structural dynamics; (4) Multi-resolution: To address the scale disparity between large fluid domains and thin flexible structures, a multi-resolution strategy is incorporated to locally refine structural particles. Furthermore, a multiple time-stepping scheme is adopted to assign distinct integration steps for fluid/soil and solid phases, significantly boosting computational performance. The framework is validated against diverse 3D benchmarks, including U-tube seepage flow, submerged landslide-generated waves, and ball impacts on granular beds, etc. Finally, its practical capability is demonstrated through the simulation of a 3D real-terrain bouldery debris flow impacting a flexible barrier, showcasing its potential for analysing complex geohazards.