The position estimation and formation configuration planning problem of multiple spacecraft is addressed in this study. Firstly, a dynamic model is established for satellite formation flight. Subsequently, a real-time fusion positioning method based on Extended Kalman Filtering and Nonlinear Least Squares is proposed to process inter-satellite distance measurements, enabling real-time high-precision positioning. To address the formation maintenance issue, linear quadratic optimal controllers are designed for two typical thruster models based on reasonable linearization assumptions. Finally, external perturbations are introduced, and simulations are conducted to validate the rationality of the controller design. The simulation results demonstrate that the proposed real-time positioning algorithm exhibits superior noise reduction capabilities compared to traditional positioning methods. Additionally, the designed formation maintenance controller, which considers practical operational constraints, provides more practical guidance than conventional formation maintenance approaches.