The pump-stopping water hammer caused by accidental power failure is one of the main threats to the safe operation of pump station project. For long-distance negative-lift pump station (LDNLPS) with downstream water level lower than upstream water level, accidental pump stop can easily cause pipeline emptying, which makes it challenging to protect against negative water hammer. It is crucial to investigate hydraulic control measures for pump stop conditions. Taking a LDNLPS as a case study, we simulated the hydraulic transients under accidental pump stop and valve rejection conditions. We compared and analyzed the water hammer protection effects of three hydraulic control schemes: air tank, air valve, and combination of air valve with air-valve surge chamber. The results indicate that using air tank requires large volume and high investment costs; air valve alone struggles to address the large negative pressure at local high points of the pipeline and may still induce bridging water hammer. Conversely, combining some air valves with short pipes to form air valve surge chamber effectively controls the negative pressure in the pipeline. In conclusion, the combination of air valve with air-valve surge chamber is economical and effective in protecting against water hammer, hence offering a viable solution for hydraulic control in similar LDNLPS projects.