Abstract: Bottom roughness analysis is a key process in design, construction and operation maintenance of subsea freespanning pipeline. In this paper, a new analysis procedure is proposed using the vector form intrinsic finite element(VFIFE) method. In this procedure, the UWAPIPE model is used to simulate the pipe-soil interaction, and the domain decomposition MPI parallel computing technique is adopted to increase efficiency. A pipeline through sandwave region in South China Sea is simulated to identify the pipeline configuration, the status of free spanning and the distribution of bending moment. Comparison shows that the simulated results agree with the survey results by remote operated vehicle(ROV). In this regard, based on the statistical analysis of the free-spanning data, the spanning heights and lengths in different work conditions are determined. Moreover, since free-spanning pipeline is dangerous, pipeline lowering is simulated. Results show that the pipeline lowering method can effectively avoid free-spanning and reduce distribution of bending moment in pipeline. This method may be applied in safety warning for long-distance subsea pipeline.