Non-chrome metal tanned waste leather shavings were used as raw materials to be degraded by hydrogen peroxide catalytic oxidation for preparing bio-based protein filler. The degraded collagen hydrolysate (DCH) was then modified with dialdehyde sodium alginate (DSA) to prepare bio-based DCH (BDH). The structure and properties of DCH and BDH were characterized by FTIR, GPC, XPS and Zeta potential test. The results showed that DSA successfully modified DCH, and the weight-average molecular weight of BDH was increased from 3900 g/mol of DCH to 5570 g/mol as well as its isoelectric point was changed from 5.2 to 3.3. Compared with the crust leather without filling by protein filler, the properties of DCH and BDH filled crust leathers were significantly better, especially the tensile strength and fullness. Compared with the DCH filled crust leather, the tensile strength of BDH filled crust leather increased from 11.5 N/mm2 to 22.9 N/mm2, its tear strength increased from 58.1 N/mm to 80.9 N/mm and the softness increased from 7.2 mm to 7.9 mm. Besides, the fullness of BDH filled crust leather was further improved. Overall, the above-mentioned properties were better than those of crust leather filled using common commercial protein filler.