Facility-based agriculture has rapidly advanced due to its capacity for high-intensity and year-round crop cultivation. This study evaluated the effects of different nitrogen fertilizer application rates on the growth of greenhouse tomatoes, while utilizing ¹⁵N tracing technology to explore nitrogen utilization efficiency during the growth process of facility-grown tomatoes. The results indicate that nitrogen application rates within the range of N60–N80 (93–128 kg N ha⁻¹) can optimally balance yield, nitrogen-use efficiency, and crop growth. Application rates exceeding this range do not enhance yield and lead to reduced nitrogen-use efficiency. Tomato plants exhibited a low N requirement during the seedling stage, relying primarily on native soil N stocks during the flowering stage. Fertilizer-derived N use increased during the fruiting stage. These findings demonstrate that excessive N inputs lead to diminishing returns and potential nutrient imbalances, while fully utilizing soil N stocks during the seedling and flowering stages is essential. This study emphasizes the importance of adjusting nitrogen input according to the developmental stages of the crop to optimize yield and resource utilization.