This paper constructed a stacked-autoencoder neural network model (SAE model) to estimate sea state bias (SSB) based on radar altimeter data. Six cycles of the geophysical data record (GDR) from Jason-1/2 radar altimeters were used as a training dataset, and the other 2 cycles of the GDR from Jason-1/2 were used for testing. The inputs to this SAE model include the significant wave height (SWH), wind speed (U), sea surface height (SSH), backscatter coefficient (σ0) and automatic gain control (AGC), and the model outputs the SSB. The model includes one input layer, three hidden layers and one output layer. The SSBs in the GDR of Jason-1/2 were obtained from a nonparametric model based on the SWH and U as input variables; thus, the model has high accuracy but low efficiency. The SSBs in the GDR of HY-2A were computed using a four-parameter parametric model that uses the SWH and U as input variables; therefore, this model's computational speed is high but its accuracy is low. Thus, we used the HY-2A radar altimeter as an unseen validation dataset to evaluate the performance of the SAE model. Then, we analyzed the contrasting results of these methods, including the differences in the SSB, explained variance, residual error and operational efficiency. The results demonstrate not only that the accuracy of the SAE model is superior to that of the conventional parametric model but also that its operational efficiency is better than that of the nonparametric model.