Owing to the complexity of the pipe-in-pipe (PIP) riser system in structure, load and restraint, many problems arise in the structural analysis of the system. This paper presents a new method for nonlinear static finite element stress analysis of the PIP riser system. The finite element (FE) model of the PIP riser system is built via software AutoPIPE 6.1. According to the specialties of a variety of components in the PIP riser system, different elements are used so as to model the system accurately. Allowing for the complication in modeling the effects of seabed restraint, a technique based on the bilinear spring concept is developed to calculate the soil properties. Then, based on a pipeline project, the entire procedure of stress analysis is discussed in detail, including creation of an FE model, processing of input data and analysis of results. A wide range of loading schemes is investigated to ascertain that the stresses remain within the acceptable range of the pipe material strength. Finally, the effects of the location of flanges, the thermal expansion of submarine pipelines and the seabed restraint on stress distribution in the riser and expansion loop are studied, which are valuable for pipeline designers.