To detect the occurrence of ionospheric scintillation in the equatorial region, a coherent/non-coherent integration method is adopted on the accumulation of intermediate frequency (IF) signal and local code, in the process of signal acquisition based on software receiver. The processes of polynomial fitting and sixth-order Butterworth filtering are introduced to detrend the tracking results. Combining with ionospheric scintillation detection algorithm and preset thresholds, signal acquisition and tracking, scintillation detection, positioning solution are realized under the influence of strong iono-spheric scintillation. Under the condition that the preset threshold of amplitude and carrier phase scintillation indices are set to 0.5 and 0.15, and the percentage of scintillation occurrence is 50%, respectively, PRN 12 and 31 affected by strong amplitude scintillation are detected effectively. Results show that the positioning errors in the horizontal direction are below 5m approximately. The software receiver holds performances of accurate acquisition, tracking and positioning on the strong ionospheric scintillation conditions, which can provide important basis and helpful guidance for relevant research on ionospheric scintillation, space weather and receiver design with high performance.