The submerged floating pipeline is floating at a certain ocean depth with tethers anchored to the seabed. This novel concept of pipeline can be a promising solution for challenging seabed conditions. Because the pipeline is floating at the mid-deep water and does not interact directly with the seabed, there is no need to do any seabed intervention work and wave forces on the pipeline can also be ignored. But the dynamic response of this type of pipeline under strong currents poses several challenges for design of floating pipeline. This work investigates the parametric resonance of submerged floating pipeline between two floating structures. The parametric resonance can lead to the huge motions and fatigue damage of the pipeline. Thus, it is essential to investigate the parametric resonance of the submerged floating pipeline system under combined parametric and vortex excitations considering uncertainties. Hill’s equation of dynamic responses of the pipeline are derived and hill stability diagrams are used to analyses the corresponding motion stability. The effect of the significant uncertain factors on the probability of the parametric stability is investigated using the metamodel method. According to analyses, some effective measures are given to the designers to avoid the parametric instability for the submerged floating pipeline design.