Freshwater scarcity in southern Xinjiang has intensified the need for effective utilization of saline–alkaline agricultural drainage. This study evaluates pre-treatment technologies for reverse osmosis (RO) systems to improve water quality and mitigate membrane fouling. Three processes were tested: coagulation–sedimentation–media filtration (G₁), micro-flocculation–media filtration (G₂), and micro-flocculation (G₃) combined with ultrafiltration and varying polyaluminum chloride (PAC) dosages (0–15 mg·L⁻¹). Results show that G₁ and G₂ significantly outperform G₃ in removing turbidity, organic matter, and inorganic ions, achieving SDI₁₅ < 5 and turbidity < 0.3 NTU, meeting RO feedwater standards. Optimal performance occurred at the 7.5–10 mg·L⁻¹ coagulant dosage range, effectively controlling flux decline and fouling. The integrated pre-treatment–ultrafiltration system provides a robust technical framework for saline–alkaline water desalination, offering practical guidance for sustainable water resource utilization in arid agricultural regions.