Efficient decontamination of heavy metals from water remains an urgent and still challenging issue. Herein, a novel adsorbent HMO@N001 was prepared by the in-situ encapsulation of hydrated manganese(IV) oxides (HMO) NPs inside the gel-type cation exchanger N001. Owing to the < 5 nm swollen pores of the N001 host, the in-situ growth of HMO NPs was restricted to sub-5 nm level (with the average size of 4.65 ± 1.17 nm). As a comparison, HMO NPs inside the commercially available macroporous analogue HMO@D001 possessed the average size of 24.52 ± 5.07 nm. The sub-5 nm nature granted HMO@N001 higher proportion (56.7%) of the reactive terminal oxygen (Mn-OH) compared with HMO@D001 (42.7%), contributing to that the maximum adsorption capacities (Qm) of HMO@N001 (146.6 ± 2.8 mg/g) toward Ni(II) reached to ∼1.36 times the value of HMO@D001 (107.9 ± 7.6 mg/g). Common coexisting cations including Na+, Mg2+, and Ca2+ mainly suppressed the electrostatic adsorption from the N001 host, while the inner-sphere complexation between Ni(II) and HMO NPs was little affected, as verified by the SEM-EDS analysis. The used HMO@N001 was effectively regenerated using 0.05 M dimethylglyoxime solution for cyclic utilization. In fixed-bed experiments, the effective treatment capacity of the HMO@N001 column reached up to ∼4200 bed volume (BV), over 1.35 times that of the HMO@D001 column (∼3100 BV). This study may provide a promising option for advanced heavy metals decontamination.