The invention discloses a special water conservation type rhizosphere fertilizer for flue-cured tobacco seedlings. The fertilizer is prepared from, by mass, isobutylidene diurea, potassium magnesium phosphate, nitrate of potash, a potassium humate organic and inorganic water-retaining agent, sodium borate, zinc oxide, blue vitriol, ferrous sulfate, manganese sulfate, ammonium molybdate, limestoneflour, chitosan and a root growth promoting agent. The special water conservation type rhizosphere fertilizer is adopted to spray the seedlings at the outsides of flue-cured tobacco roots, one-time fertilizer applying is achieved on the flue-cured tobacco seedlings, compared with a traditional seeding growing mode, fertilizer applying of 2-3 times is reduced, and the fertilizer applying amount isreduced by 20-30%; the biomass of the grown flue-cured tobacco seedlings is increased by 15% or above, and the tobacco seedling root shoot ratio is improved by 20% or above; the total root lengths ofthe grown seedlings are improved by 150% or above, the common root area is increased by 30% or above, the stem diameter is increased by 20% or above, and the strong seedling index is improved by 30% or above. Therefore, the fertilizer has the effects of significantly reducing the fertilizer applying amount for the flue-cured tobacco seedlings and improving the agricultural labor productivity efficiency and the economic benefit, and has a wide market prospect.