Transitioning heat exchanger network (HEN) synthesis designs to industrial application involves operational, environmental, and cost considerations, posing computational challenges. This study proposes a systematic optimization approach integrating multi-objective, multi-period optimization HEN synthesis with waste heat recovery and multiple utilities. The proposed methodology incorporates a novel two-step unit reduction strategy to overcome the increase of model combinational complexities arisen from the multi-period features, thereby facilitating the solving of large-scale problems. Meanwhile, environmental impacts are concerned by using the technique for order preference by similarity to ideal solution approach. A new optimization route, Enhanced Pinch-assisted Multi-Objective Optimization is proposed to obtain the final decision in this multi-objective problem time-efficiently. The case study includes a 15 streams problem, and a real industrial-scale crude oil distillation preheat system. The results showed that assigning carbon compensation to the waste heat recovery option can significantly reduce carbon emissions and change energy distribution.