Nitrogen-modulated intercropping boosts yield and quality in Codonopsis pilosula

Intensive monoculture of Codonopsis pilosula (C. pilosula) reliant on high nitrogen (N) inputs often compromises root quality and long-term sustainability. Here we show that intercropping with faba bean under optimized N application resolves this trade-off by enhancing root yield and the accumulation of active ingredients. To test this, we established a two-factor factorial design with monoculture vs. intercropping across three N rates (0, 60, 120 kg N ha⁻1). Root yield, concentrations of three key active ingredients (lobetyolin, atractylenolide III, and syringin), leaf traits, photosynthetic parameters, and the activities of key carbon and nitrogen metabolic enzyme were measured. Intercropping increased root yield by 3.2%-18.7%, active ingredient concentrations by 5.5%-56.9%, and active ingredients yield by 29.7%-47.1%. Mechanistically, these improvements were associated with key physiological changes: 1) enhanced photosynthetic capacity (larger leaves with higher photosynthetic rate) increasing total carbon assimilation; 2) upregulated C/N metabolism strengthening utilization and storage capacity of photosynthetic assimilates in root. These benefits were achieved despite a decrease in instantaneous water use efficiency, a pattern consistent with a “water-for-carbon” strategy at the leaf level. The intercropping advantage for C. pilosula was maximized at 60 kg N ha−1, while excessive N application (120 kg N ha−1) diminished these benefits and reduced active ingredient concentrations. Our findings demonstrate that faba bean intercropping under moderate N promotes both productivity and medicinal quality of C. pilosula by co-optimizing leaf physiology and C/N metabolism, providing a potential strategy for more sustainable cultivation under the conditions tested.