Molybdenum disulfide (MoS2), a graphene-like two-dimensional layered material, exhibits a great application prospect in high-performance energy storage devices. To overcome poor electrical conductivity and large volume change of pure MoS2 material, we herein apply an effective encapsulation strategy to prepare a core-shell structured MoS2@mesoporous hollow carbon spheres nanocomposite, which is used as an excellent electrode material for aqueous supercapacitors and hybrid Li-ion capacitors for the first time. The results indicate that mesoporous hollow carbon spheres shell not only effectively confines the growth of MoS2 nanosheets inside shells, but also improve significantly the conductivity and structural stability of the nanocomposite. The nanocomposite electrode delivers a high specific capacitance (613.4 F g−1 at 1 A g−1) and good rate performance (358.2 F g−1 at 10 A g−1) as well as excellent cycle performance for aqueous supercapacitors. More importantly, an ultrahigh specific energy density of 208 Wh kg−1 at 200 W kg−1 (82 Wh kg−1 at 10,000 W kg−1) is demonstrated for hybrid Li-ion capacitors based on the nanocomposite anode. The observed specific energy density is among the highest values reported to date.