The valve-controlled hydraulic cylinder system (VCHCS) is commonly used for actuators such as manipulators in deep-sea equipment, whose working performance is crucial to subsea tasks. Affected by the ambient pressure introduced by the pressure compensator, the viscosity of the hydraulic oil increases significantly. On this basis, the viscosity changes further when flowing in the slender pipeline, making the pipeline pressure loss substantially increase and subsequently affecting the working performance of the deep-sea VCHCS. Aiming at this issue, a detailed nonlinear mathematical model of the deep-sea VCHCS is established, in which the viscosity-pressure characteristics of the hydraulic oil is considered to take the viscosity changes in the pipeline into account. Besides, the hydrodynamic effects are also included in the model. Then the corresponding numerical simulation model of the deep-sea VCHCS is established, and its working performance at different depths is simulated and analyzed. When the depth is 11km, the extension and retraction movements are delayed by 52.50% and 43.12% respectively. The root cause of the delay is then analyzed and discussed. Finally, the parameters that affect the working performance are studied, and suggestions to reduce or eliminate the delay phenomenon are given. The results can provide theoretical support for the performance optimization of the deep-sea VCHCS.