The inevitable inorganic fouling in saline water drip irrigation systems (SWDIS) with phosphorus fertilizer has become key obstacle for utilizing saline water and phosphate fertilizer. This study developed a greener anti-fouling method by intelligently applying a superior fertilizer (i.e. ammonium polyphosphate, APP). X-ray diffractions and Rietveld refinement method were used to determine the mineral composition and cell parameters of scales. Results showed that APP effectively minimized the inorganic fouling in SWDIS, with the fixed scales quantity reduced by 17.8–59.3%. Consequently, the average discharge and fertigation uniformity of SWIDS in APP groups were 26.4–49.5% and 40.5–63.5% higher than that in no-fertilizer groups. The aragonite and calcite contents were decreased by 52.9–63.7% and 35.3–53.3% with APP application, which was because of APP chelating salt cations (e.g., Ca2+) to decrease the probability of carbonates formation. In addition, APP increased the cell volumes of aragonite and calcite to 0.26–5.33A3, which resulted in the retrogression of crystallinity and phase purity. Moreover, compared with lower concentration with long time fertigation mode, the scales’ contents in higher concentration with shorter time fertigation mode reduced by 20.9%. This study proposes an effective, eco-friendly fertigation method to control the inorganic fouling in SWDIS, which provide a new perspective for the sustainable management of saline water and phosphorus fertilizer in arid areas.