Rice (Oryza sativa L.) plays a pivotal role in global food security, yet its breeding is constrained by its long generation time and seasonality. To enhance rice breeding efficiency and meet future food demands, we have developed a vertical hydroponic breeding system integrated with light-emitting diodes (LEDs) lighting in a closed plant factory (PF), which significantly accelerates rice growth and generation advancement. The results show that indica rice can be harvested as early as after 63 days of cultivation, a 50% reduction compared with field cultivation, enabling the annual harvesting of 5–6 generations within the PF. A hyperspectral imaging (HSI) system and attenuated total reflectance (ATR) infrared (IR) spectroscopy were further employed to characterize the chemical composition of the PF- and field-cultivated rice. Metabolomics analysis with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) and gas chromatography-mass spectrometry (GC-MS) revealed that, compared with the field-cultivated rice, the PF-cultivated rice exhibited an up-regulation of total phenolic acids along with 68 non-volatile and 19 volatile metabolites, such as isovitexin, succinic acid, and methylillicinone F. Overall, this study reveals the unique metabolic profile of PF-cultivated rice and highlights the potential of PFs to accelerate the breeding of crops such as rice, offering an innovative agricultural strategy to support food security in the face of global population growth and climate change.