Reliable operation of adjustable ballast systems is essential for full-ocean-depth manned submersibles, but existing studies mostly focus on component-level performance optimization, leaving the multi-valve coupled instability mechanism under ultra-high pressure insufficiently understood. This paper investigates an uncontrolled water injection failure in the adjustable ballast system of the “Fendouzhe” submersible via fault tree analysis, high-pressure physical tests and AMESim dynamic simulations. Results show that the initial fit clearance of the downstream flow valve is the dominant prerequisite for instability, and a fluid–structure interaction positive feedback loop between the series valve assembly drives the flow surge fault. Removing the series flow valve fundamentally interrupts the coupling feedback loop. Full-range 0–115 MPa bench tests and follow-up sea trials confirm that the modified system eliminates the observed flow surge within the tested pressure range and operating conditions. This work provides a practical diagnostic framework and engineering reference for reliability design of high-pressure seawater hydraulic systems.