A multi-scale habitat information-based method and device for detecting and controlling water and fertilizer for crops in seedling stage: performing fusion analysis on multi-scale features of the water and fertilizer stress of crops on the basis of crop canopy-scale three-dimensional laser scanning information, foliage-scale polarization-hyperspectral imaging information, and micro-scale micro-CT scanning information; combining the real-time feedback of the temperature, humidity, illumination and substrate moisture content within a crop growing greenhouse; by means of multi-information fusion modeling, comprehensively determining and feeding back the water and fertilizer stress of the crops as well as water requirement and fertilizer requirement information, and providing policy information for the amount of fertilization and irrigation. On the basis of the policy information for water and fertilizer, and on the basis of frequency conversion speed control technology and pipeline constant pressure control technology, a water and fertilizer control system controls the pressure of a pipeline and the flow rate of the fertilizer by means of dynamically controlling the rotation speed of an irrigation pump and a fertilizer pump, and thus, combined with the dynamic feedback of an EC value, the accurate control of a liquid fertilizer ratio and irrigation volume is achieved.