In order to increase the thermostability and catalytic efficiency of acidophilic GH11 xylanase, two disulfide bonds were introduced into crucial region of the enzyme. The xylanase PjxA, from Penicillium janthinellum MA21601, has attracted considerable attention due to its favorable acid-resistance; however, its poor thermostability and low enzymatic hydrolysis efficiency limit its application. In this study, two disulfide bonds were introduced into crucial regions of three recombined xylanases (DB-s1s3, DB-s1s4, and DB-s3s4). All three xylanases remained acid-resistant while gaining improved hydrolytic and thermostability properties, of which DB-s1s3 was the most noteworthy. The optimal temperature of recombined xylanase DB-s1s3 increased from 50 °C to 70 °C. The specific activity of DB-s1s3 was 4.76-fold higher than that of wild-type xylanase PjxA. Moreover, DB-s1s3 showed a 2.14-fold increase in kcat/Km. In addition, DB-s1 s3 showed improved hydrolytic characteristics, of which the most noteworthy was its enhanced ability to produce xylose and xylobiose from polymeric substrates. Compared with PjxA, combining DB-s1 s3 with cellulase improved the hydrolytic yield of corncob powder, procuring concentrations of xylose (X1) and xylobiose (X2) of 204.4% and 24.4%, respectively. Thus, these mutants offer great potential for application in the agricultural residue degradation industry.