Deepwater surface BOP (surface blowout prevention, SBOP) drilling differs from conventional riser drilling system. To analyze the dynamic response of this system, the riser-conductor was considered as a beam with varied cross-sections subjected to loads throughout its length; then an equation of motion and free vibration of the riser-conductor string for SBOP was developed. The finite difference method was used to solve the equation of motion in time domain and a semianalytical approach based on the concept of section division and continuation was proposed to analyze free vibration. Case simulation results show that the method established for SBOP system natural frequency analysis is reasonable. The mode shapes of the riser-conductor are different between coupled and decoupled methods. The soil types surrounding the conductor under mudline have tiny effect on the natural frequency. Given that some papers have discussed the response of the SBOP riser, this work focused on the comparison of the dynamic responses on the wellhead and conductor with variable conditions. The dynamic lateral displacement, the bending moment, and the parameters' sensitivity of the wellhead and the conductor were analyzed.