Deepwater drilling has the problem of narrow safe density window, and double-layer pipe dual-gradient drilling is one of the effective ways to solve the narrow safe density window. Due to the different structure and process principle with MPD, there is an urgent need to establish the hydraulic model and control algorithm of double-layer pipe dual-gradient drilling in order to realize the normal regulation of bottom hole pressure during drilling. Based on the hydraulic theory of managed pressure drilling and considering the influence of the three-channel structure of double-layer pipe and the downhole hydraulic lift pump in double-layer pipe dual-gradient drilling, a hydraulic model of double-layer pipe dual-gradient drilling has been established and verified in land well tests. Based on the double-layer pipe dual-gradient drilling hydraulic model, a control algorithm based on pressure regulation and flow rate regulation is established considering the principle of double-layer pipe dual-gradient drilling process. The simulation results show that the control algorithm based on flow rate regulation can greatly reduce the bottom hole pressure regulation time by controlling the size of the flow rate of the return fluid. When the bottom hole pressure is increased from 25 MPa to 26 MPa, the regulation time is 11min, which basically meets the requirements of field operation. The hydraulic model and control algorithm of double-layer pipe dual-gradient drilling are favorable to the bottom hole pressure regulation during drilling and reduce the response time.