To address the accuracy divergence problem of the integrated navigation system caused by drilling slippage and mismatch between the tail cable encoder and the robot's motion when a seafloor drilling robot operates in deep-sea soft sedimentary layers, this paper proposes a robust navigation method based on robust square root ductile Kalman filter (RSRCKF). Considering the large deformation mechanical characteristics of the seabed under drilling conditions, a unified state-space model including the time-varying odometer scaling factor error is first established. To solve the numerical instability of the nonlinear system under non-Gaussian noise interference, the square root ductile Kalman filter (SRCKF) framework is introduced, and the positive definiteness of the error covariance matrix is dynamically maintained using QR decomposition. Based on this, an online fault detection mechanism based on the novel chi-square test is designed, and an adaptive variance expansion factor is constructed by combining a two-segment IGG weight function to realize the real-time identification and weight reduction processing of abnormal observations caused by slippage. Field drilling and turning tests on the mudflats off the coast of Zhoushan show that, under typical soft clay slippage conditions, this method can effectively identify "false displacement" interference. Compared with the traditional EKF and standard SRCKF, the position error is reduced by approximately 82.4%, and the heading angle error is controlled within±0.5∘Within a certain range, the high robustness and engineering practicality of the algorithm under complex seabed topography were verified.