Other than lights, the main factors affecting seedling growth in nurseries are moisture and fertilizer. This study aimed to reveal the response mechanism of Lonicera caeruleae seedlings to the coupling effect of water and fertilizer and to provide a theoretical basis for improving L. caeruleae quality and yield. The cuttings of one-year-old seedlings were used in a pot experiment with a quadratic rotation regression design with five levels of three factors that was carried out in a greenhouse. The results show that nitrogen application amount, phosphorus application amount, and soil water content had significant positive effects on the content of various substances in seedlings, and water-nitrogen coupling and water-phosphorus coupling had significant effects on the content of osmotic regulatory substances in seedlings. The soluble proteins and sugars in seedlings were significantly positively affected, whereas both proline and malondialdehyde were significantly negatively affected. The model results provided an optimal solution to the equation, and the following combination of water and fertilizer substantially improved seedling growth: soil moisture at 71.3% of field water capacity, nitrogen fertilizer at 7.516 g/plant, and phosphorus fertilizer at 6.573 g/plant. In conclusion, using these parameter estimates could optimize water and fertilizer application for L. caeruleae seedlings.