Retrofitting industrial heat recovery systems is a key pathway toward low-carbon and resource-efficient manufacturing. Integrating waste heat recovery (WR) with multiple utility (MU) networks can significantly improve energy efficiency, but also creates strong coupling between process heat recovery, waste heat utilisation, and utility allocation. However, existing approaches often address these elements separately or sequentially, limiting the ability to identify optimal system-level retrofit solutions. This study aims to develop a system-level optimisation framework to resolve trade-offs between waste heat recovery and multiple utility integration in industrial retrofit. The framework allows for (i) modifying existing exchangers, (ii) installing new process-to-process units to enhance heat recovery, (iii) integrating waste heat recovery systems for generating high-pressure steam, low-pressure steam, and hot water, and (iv) incorporating optimal utilisation of multiple utilities. The framework is validated through two large-scale industrial case studies. In Case 1, WR and MU integration reduce utility cost to 9.8E+06 $/y (64.6% below the original design) and GHG emissions from 1.7E+08 to 1.2E+08 kg/y CO2 (30.3% reduction), with hot water generation contributing 82.7% of savings. In Case 2, the same strategy achieves a 45.6% GHG reduction relative to the baseline and lowers operation costs by 28.9%. This work provides a practical, system-level retrofit framework to support sustainable production and low-carbon transition in industrial processes.