In present research, the problem of vortexinduced vibration (VIV) of marine riser structure with complex prestress force distribution is considered. Based on the EulerBernoulli beam theory, according to the stressstrain formula, differential equations of the influence with complex prestress force distribution on riser structure are established. At the end, a toptensioned riser (TTR) which is under shear flow loading is taken as an example, the influence of natural frequency, mode shape, and VIV response characteristic by complex prestress force distribution are investigated. The result shows that the distribution of complex prestress force has a significant influence on the riser structural dynamic characteristics, especially on the natural frequency. It is shown that the method proposed in this research provides a new approach to analyze the VIV problem of riser structure with complex loading.