The high-throughput immobilized metal affinity chromatography (IMAC) material is urgently required to improve the efficiency of separation and purification of tagged-peptides in the related biomedical applications. Herein, the aminothiourea-modified nanocellulose (S-TOCN)-polyvinyl alcohol (PVA) composite aerogel with aligned pores was fabricated by directional freezing casting technique and then used to immobilize metal ion for the selective separation and purification of histidine-containing peptides from protein hydrolysates. The obtained S-TOCN-PVA materials with an oriented porous structure under the optimal conditions exhibited excellent mechanical properties, good adsorption performance and reusability. The adsorption capacity of S-TOCN-PVA aerogel for metal ions were as follows: Cu2+>Ni2+>Zn2+>Co2+, in which the higher metal ion chelating amount of S-TOCN-PVA composite aerogel for Cu2+ and Ni2+ reached 87.21 mg/g at pH=7 and 83.66 mg/g at pH=6 in the 2 h incubation time, respectively. The enrichment effects of Cu2+/S-TOCN-PVA and Ni2+/S-TOCN-PVA aerogels with selectivity of His-containing peptides from apricot kernel protein hydrolysates were up to 3.99 folds and 4.81 folds for one cycle, respectively. Moreover, the Ni2+/S-TOCN-PVA aerogels retained 87.5% of their initial adsorption capacity (848 mg/g) after 5 cycles, and the concentration was raised 39.05 folds. Molecular docking simulation showed that the oxygen of carboxyl group (-C-O and -C=O) and hydrogen of imidazole group at His molecule was primarily bound to the hydrogen of amino groups and oxygen of carboxyl group (C-O-C) on the structure of M2+/S-TOCN-PVA aerogels. The fabricated metal ion immobilized 3D aligned porous nanocellulose-based aerogels can be used as IMAC materials for rapid separation and purification of histidine-containing polypeptides from complicated biological samples.