Abstract: Considering the shut-in status of offshore oil and gas wells, the separation of oil and gas under gravity in flexible riser leads to nonuniform distribution of tension in riser. A simplified mathematical model is established for lateral vibration of connected marine riser with variety tension along depth. Based on the variable separation method, the expression of the natural frequency and corresponding modal function of riser lateral vibration under shut-in status are given in terms of Bessel functions. By analyzing the influence of oil–gas ratio, density and top tension on the natural frequency and modal function of vibration, we find that the natural frequency of horizontal vibration of the riser increases gradually, and the maximum antinode of modal function moves to the deep water as the length of riser containing the gas segment in the flexible riser increases. Compared with the working status, the natural vibration frequency of the riser decreases when the well is shut in and stratified. With the increase of liquid density in flexible riser, the natural frequency of vertical vibration increases gradually. As the top tension provided by offshore platforms increases, the natural frequency gradually increases.