Combine harvesting has become widespread in northern Iran, improving efficiency but creating bottlenecks in drying capacity. This often leads to delayed drying and intermediate storage of high-moisture paddy, risking quality deterioration. This study investigated the effects of pre-drying temperature and storage duration on the milling quality of Hashemi rice, a major Iranian variety. Freshly harvested paddy (~20% moisture, w.b.) was pre-dried in a recirculating dryer at 40, 50, or 60 °C to 15% moisture, then stored for 15, 30, or 45 days before undergoing final drying in a conventional batch dryer to 8.5% moisture. A factorial experiment based on a randomized complete block design (RCBD) with five replications was conducted. Results showed that both pre-drying temperature and storage duration significantly affected head rice yield (HRY) and grain fissure percentage (p < 0.01). Increasing the pre-drying temperature from 40 °C to 60 °C reduced HRY by approximately 2% and increased fissures by 3%. Similarly, extending storage from 15 to 45 days reduced HRY by 2.6% and increased fissures by 4.7%. Milling recovery was not significantly affected. These findings highlight that high-temperature pre-drying and prolonged intermediate storage negatively impact grain integrity. To optimize milling quality, it is recommended to use moderate pre-drying temperatures (≤40 °C) and minimize the time between pre- and final drying stages.