An efficient double-chitinase hydrolysis of crab shell particles (CSP) pretreated by ionic liquids was investigated in this work. First, two family 18 chitinase genes (chip1 and chip2) from Paenibacillus pasadenensis CS0611 were cloned and functionally expressed. The purified chip1 and chip2 showed a molecular mass of 70.2 and 48.0 kDa, respectively, by SDS-PAGE, and were optimally active at pH 5.0 and 45–55 °C. The two chitinases preferred pretreated chitin substrates to natural chitin. Then, eight ionic liquids were applied to pretreat CSP to facilitate its hydrolysis. [BMIm]Ac-treated chitin exhibited the best pretreatment efficiency as a result of weakened structure and decreased crystallinity, which was confirmed by FTIR and XRD. The SEM result also proved a morphological change of thinner fiber structure. Finally, 712.6 ± 12.5 mg/g precsp of N,N′-diacetylchitobiose and 177.1 ± 4.5 mg/g precsp of N-acetyl-glucoamine were generated from pretreated CSP in a double-chitinase hydrolysis system. This process presents a promising strategy for the production of chito-oligosccharides.