Objectives The square root unscented Kalman filter (SR-UKF) algorithm was developed for the identification of hydrodynamic coefficients, which are difficult to obtain accurately in submarine motion models. Methods Firstly, the hydrodynamic coefficients identification model was established based on the nonlinear mathematical model of submarine motion in the vertical plane, combined with the SR-UKF algorithm. Then, a sinusoidal maneuvering in the vertical plane was carried out by the automatic steering method and the generated data in addition to the measurement errors were chosen as the input for SR-UKF parameter identification. Finally, six viscous hydrodynamic coefficients in the vertical motion plane were identified through a numerical simulation. Results The simulation results show that, all identified hydrodynamic coefficients converge to fixed values within 3 000 seconds, and through the selection of appropriate initial values, the maximum error between the identification results and the standard values measured by a hydrodynamic test is only 1.5%. Conlusions SR-UKF can be effectively applied to identify submarine hydrodynamic coefficients, and can be further extended to real ship coefficients identification.