To achieve autonomous all-day flight by high-altitude long-endurance unmanned aerial vehicle (HALE UAV), a new navigation method with deep integration of strapdown inertial measurement unit (SIMU) and triple star sensors based on atmospheric refraction correction is proposed. By analysing the atmospheric refraction model, the stellar azimuth coordinate system is introduced and the coupling relationship between attitude and position is established. Based on the geometric relationship whereby all the stellar azimuth planes intersect on the common zenith direction, the sole celestial navigation system (CNS) method by stellar refraction with triple narrow fields of view (FOVs) is studied and a loss function is built to evaluate the navigation accuracy. Finally, the new SIMU/triple star sensors deep integrated navigation method with refraction correction upgraded from the traditional inertial navigation system (INS)/CNS integrated method can be established. The results of simulations show that the proposed method can effectively restrain navigation error of a HALE UAV in 24 h steady-state cruising in the stratosphere.