Niobium is a strategic critical metal. Its supply is vulnerable to geopolitical instability, which necessitates the development of novel resources. Here, we propose a novel, efficient and clean two-stage leaching process for recovering niobium from clay-weathered crust of the Emeishan basalt in the Sichuan-Yunnan-Guizhou region of southwestern China. The primary leaching involves roasting (600 °C)-sulfuric acid (20 %) leaching, which selectively dissolves the aluminium-bearing boehmite and kaolinite to concentrate the niobium-bearing anatase and illite, and simultaneously yield byproducts such as ferric hydroxide, aluminium hydroxide and ammonium sulfate. The secondary leaching utilizes the byproduct ammonium sulfate as an agent for ammonium sulfate roasting (450 °C), which couples with sulfuric acid (35 %) leaching to enhance niobium extraction. This gives a maximum extraction efficiency of 91.06 %. Thermodynamic analysis revealed that ammonium bisulfate (thermal decomposition product of ammonium sulfate) can spontaneously decompose niobium-bearing minerals (anatase and illite) (ΔG^θ<0), thereby releasing niobium to form the soluble niobium trioxysulfate. Subsequent leaching with 35 % sulfuric acid enables highly efficient niobium extraction. Kinetic analysis demonstrated that the niobium leaching process is jointly controlled by interface transfer and diffusion through the inert product layer (E_a = 50.54 kJ/mol). Efficient absorption of exhaust gases with sulfuric acid and ammonia would minimize air pollution, and the final leaching residue comprises mainly ammonium aluminum sulfate dodecahydrate (ammonium alum). This minimizes solid waste production. The technique integrates high extraction efficiency, low environmental impact, and comprehensive resource utilization, which facilitates sustainable development of refractory niobium resource.