The preparation of vanillin with clove oil as the substrate and soybean lipoxygenase (SBLOX) as the bio-catalyst has been carried out in a silicon rubber membrane bioreactor (SRMBR). Compared with ferment in shaking flasks, the SRMBR system effectively prevented the product inhibition and oxidation of vanillin, owing to separation in situ through silicon rubber membrane. The bioconversion rate of clove oil was increased to 1.01% from 0.038%. By high performance liquid chromatography (HPLC) analysis, the vanillin concentration of the receiving solution in membrane down-stream reached up to 121.53 mg/L, which was much higher than the 8.14 mg/L in the broth of the shaking flask ferment, and the peak area ratio of vanillin in the receiving solution is 70.08%. By adding activated carbon as adsorbent into the broth, the bioconversion rate of clove oil was increased further to 1.14%, the vanillin concentration in the receiving solution reached 140.27 mg/L, and the peak area ratio of vanillin in the receiving solution has amounted to 93.53%.