Thermoplastic polyurethane (TPU) is essential in resource exploration, healthcare, automotive, and high-end recreational sports. Despite extensive research on TPU's microstructures and their macroscopic properties, the impact of processing conditions like compression and injection molding remains underexplored. This study investigates the influence of processing conditions on TPU by preparing samples with varying hard segment contents using compression molding at 205 °C and injection molding at melt temperatures of 205, 210, 215, and 220 °C, followed by heat treatment at 120 °C for 12 h. Results indicate that injection-molded TPU at 205 °C exhibits lower hydrogen bonding, crystallinity, long period, interfacial thickness, and lamella thickness than compression-molded TPU, leading to higher Young's modulus but lower elongation at break. As melt temperatures increase, these microstructural parameters decrease, reducing Young's modulus and increasing elongation at break. Post heat treatment, microstructural parameters increase, aligning Young's modulus with that of compression-molded samples, while elongation at break surpasses them. This suggests that heat treatment enhances microphase separation by rearranging hard and soft segments. our research reveals a consistent pattern across TPUs with varying hard segment contents, indicating that adjusting processing parameters can effectively regulate microstructure and performance, offering valuable insights for developing high-performance polyurethanes.