With the increase of continuous cropping years, the physical and chemical properties of greenhouse soil is deteriorating, the proportion of nutrients is out of balance gradually, the secondary stalinization of soil is increasing, and the production performance is reducing more and more seriously. In this study, under the condition of straw returning to field at 800 kg/hm², the subsurface pipe drainage system was used to investigate the effects of different pipe spacing (2, 4 and 6 m) on organic matter content, available nutrients (available nitrogen, available phosphorus and available potassium) and salt content in surface soil (0–15cm) as well as the quality of cut chrysanthemum ‘Jimba’. The results showed that the subsurface pipe drainage system significantly enhanced the root activity of cut chrysanthemum and had a positive improvement in the quality of cut chrysanthemum (plant height, stem diameter, flower diameter, ray floret number and shoot dry weight). Among the treatments evaluated, 4 m pipe spacing treatment improved soil organic matter and available nutrient contents more significantly compared with 2 m and 6 m pipe spacing treatments. 4 m pipe spacing not only had positive effects on groundwater depth controlling and desalination, but also had significant effect on reducing water content, electrical conductivity, total salt content and the main salt ions contents (Ca²⁺ and SO₄^2-) in the surface soil. With the decrease of buried pipe spacing, the effects of groundwater depth controlling and desalination became more obvious. Combined with the initial cost of embedded buried pipe into account, the treatment of 4 m pipe spacing is regarded as the most economical way to improve both soil and cut chrysanthemum qualities in continuous cropping greenhouse.