Industrial ecosystems are coupled with natural systems through utilization of feedstocks and waste disposal. To ensure resilience in production of industrial systems under the threat of climate change scenarios, it is necessary to evaluate the impact of this coupling on productivity and waste generation. In this work, we present a novel methodology for modeling and assessing the resilience of coupled natural-industrial ecosystems under climate change scenarios. We develop a computationally efficient framework that integrates liquid time-constant (LTC) neural networks as surrogate models to capture complex, nonlinear dynamics of coupled agricultural and industrial systems. The approach is demonstrated through a case study of a soybean-based biodiesel production network in Champaign County, Illinois. LTC models are trained to capture dynamics of nodes and are then coupled and driven by statistically downscaled climate projections for RCP 4.5 and 8.5 scenarios from 2006-2096. The framework enables rapid simulation of system-wide material flow dynamics and exploration of cascading effects from climate-induced disruptions. Results reveal non-linear behaviors and potential tipping points in system resilience under different climate scenarios and farm sizes. The RCP 8.5 scenario led to earlier and more frequent production failures, increased reliance on imports for smaller farms, and complex patterns of waste accumulation and stock levels. The methodology provides valuable insights into system vulnerabilities and adaptive capacities, offering decision support for enhancing the resilience and sustainability of coupled natural-industrial ecosystems in the face of climate change. The framework's adaptability suggests potential applications across various industrial ecosystems and climate-sensitive sectors