Understanding the resilience of farmland ecosystems under drought and salinization is essential for navigating agricultural trade-offs and ensuring long-term sustainability in arid northwestern China. By coupling the regionalized WHCNS model with ecological trajectory analysis, this study constructed a multidimensional state space including yield, water consumption, greenhouse gas emissions, and soil moisture, thereby quantifying the evolutionary characteristics and resilience threshold of farmland ecosystems. Finally, crop patterns in arid northwestern China were reconstructed to maximize systemic resilience and achieve optimal trade-offs. The findings indicate that: (1) Environmental conditions and crop traits jointly govern the trajectories of farmland ecosystems. Even in highly favorable, non-arid and non-salinized zones (e.g., BJ2), crops on 30.1% of farmland do not meet the resilience threshold, associated with an overemphasis on yield. This reveals a structurally vulnerable, high-yield system arising from insufficient systemic buffering. In contrast, Nanjiang converged toward a homogeneous, risk-averse steady state under strong environmental filtering. (2) Resilience-based optimization effectively resolves non-linear, multi-dimensional trade-offs. By phasing out low-stability maize (-33.7% area) and consolidating dominant crops, it established a robust crop pattern, with cotton dominance in Xinjiang and a grain-production core in the Hexi Corridor. (3) The reconstruction effects demonstrate the strategic value of trading carbon for water. Although the optimized patterns incurred a 7.8% decline in total yield and a 5.6% increase in carbon emissions, they simultaneously increased regional economic output per unit area by 3.3% and enhanced mean soil moisture content by 2.7%. This demonstrates that such strategic trade-offs fundamentally enhance the sustainable development capacity of farmland ecosystems. This study provides a framework for shifting agricultural management from yield maximization to resilience-oriented strategies. Through the resolution of multi-dimensional trade-offs and the alignment of crop traits with environmental carrying capacities, farmland ecosystems can sustain long-term viability under increasing climate uncertainty.