The cross-linked enzyme aggregates method was a new carrier-free immobilized enzyme technology. In order to improve the stability of xylanase, the technology was applied for the preparation of the acid-stable xylanase from Penicillium janthinellum. This study explored conditions of the preparation of cross-linked xylanase aggregates. The results showed that the crude xylanase at the concentration of 0.36mg/mL was precipitated with 85% saturated ammonium sulfate for 30min at 40℃. Then the aggregates were cross-linked by 0.14% glutaraldehyde solution for 4h at 40℃. The obtained activity of cross-linked xylanase aggregates remained 42.2% of total enzyme activity, which is helpful for the further application of acid xylanase in the industry.