Excessive application of fertilizers leads to the loss of a high amount of nutrients and low fertilizer utilization, which severely restricts crop productivity. Establishing better fertilizer usage practices can mitigate the adverse effects of excessive fertilizer use in agricultural practices. This study determined the effects of slow-release fertilizers on the growth; quality; root and nitrate reductase activity; accumulation; distribution of nitrogen (N), phosphorus (P), and potassium (K) in roots, stems, and leaves; and NPK utilization of winter Chinese chives (Allium tuberosum Rottler ex Spreng.) in multi-layer covered plastic greenhouses. Treatments were conventional fertilization (CF, NPK: 1369.5 kg ha−1), conventional fertilization with slow-release fertilizer (SRF, NPK: 1369.5 kg ha−1), reduced fertilization with slow-release fertilizers (SRFR, NPK: 942.0 kg ha−1), and no fertilizer arranged in a completely randomized design with three replicates. The SRFR treatment increased Chinese chives yield and economic profitability by 37% and 47%, respectively, compared to the CF treatment. Similarly, nitrate reductase activity, root activity, soluble sugar, soluble protein, and flavonoid contents in the Chinese chives were increased by 40%, 12%, 16%, 6%, and 18%, respectively, in SRFR than CF. In addition to these, we observed a significant reduction in the surplus of N (42%) and P (58%) in soil under SRFR compared to CF. Nutrient uptake and nutrient use efficiency were also greater in SRFR than in CF. The results indicate that the adoption of SRFR can be an efficient approach to enhance quality and productivity of Chinese chives compared to CF under a multi-layer covered plastic greenhouse system.