The recovery and utilization of vanadium from vanadium-bearing shale are significant, because vanadium is an important strategic metal. This study explored a cleaner metal extraction method to recover vanadium from vanadium-bearing shale using a novel strain of mutated Bacillus mucilaginosus (B.M) and an enhanced bioleaching process. The high-efficient bioleaching bacteria of B.M-0.2 was obtained by the chemical mutation of hydroxylamine hydrochloride. The optimal conditions for extracting vanadium by the mutant bacteria were 0.5g/L ammonium nitrate, 5g/L sucrose, at pH 7.5, and the ore particle size of -0.074mm accounts for 92.34%, the pulp density was 10g/L, and the vanadium leaching efficiency of B.M-0.2 was 8.16% higher than that of the original bacteria after a 30 days bioleaching period. The results showed that the mutant B.M-0.2 had the highest acid production. The total content of the organic acid produced by B.M-0.2 was nearly three times than that compared with the original strain after 2 days. The gene of the mutant B.M0.2 was sequenced by Polymerase Chain Reaction sequencing technology, and it was found that the mutant still belongs to the Bacillus family but the gene of the mutant was obviously changed. The results showed that the mutated B.M through the chemical mutation of hydroxylamine hydrochloride had great potential to improve the vanadium recovery from vanadium-bearing shale.