Ionospheric scintillation presents significant challenges to the application of Global Navigation Satellite System (GNSS) for positioning and bridge deformation monitoring in low-latitude region. This study aims to develop a GNSS positioning model to improve long-span bridge deformation monitoring performance under ionospheric scintillation. We propose a new Rate of Total Electron Content (ROT) calculation method using undifferenced estimated ionosphere delays for identifying ionospheric scintillation. Then, we construct an undifferenced and uncombined (UDUC) ionosphere-refined Real-time Kinematic (RTK) model by replacing ionospheric spatial constraints with temporal constraints to mitigate the impact of ionospheric scintillation. RTK experiments are conducted on the South China Sea Bridge (SCSB), spanning 55 km. The results indicate that the new ROT calculation method can effectively identify observations affected by ionospheric scintillation, and the ionosphere-refined RTK model shows superior performance compared to ionosphere-float and ionosphere-weighted RTK model in terms of convergence time, Time to First Fix (TTFF), and positioning accuracy.