An integrated analysis about computational time complexity of the Local Ensemble Transform Kalman Filter (LETKF) was performed. It is found that the calculation step of inverse matrix of the error covariance in ensemble space is the most computationally intensive and time consuming. In a parallel computing environment, the uneven distribution of CPU calculations in this step directly leads to low computational efficiency. To solve this problem, a new load balancing strategy was designed based on the "greedy algorithm". A high-performance parallel ocean data assimilation system based on the LETKF was developed and tested using this strategy. This system was based on the Parallel Ocean Program 2 (POP2) of the Community Earth System Model (CESM). The optimal interpolated sea surface temperature data (OISST) and Argo temperature profile data from January to February, 2004 were assimilated into the POP2. The results show that data assimilation effectively reduces the root mean square error of temperature and salinity. Using the new strategy, the exact same results are obtained but the computation time is reduced by half. At higher resolution (0.1°×0.1°),the computing performance is still doubled, indicating that this load balancing scheme is stable and reliable. In addition, the new method has high scalability and portability with great potential to be applied in operational forecasting.