Gas hydrates have been endowed with great potential as the medium for natural gas storage & transportation. In this work, we prepared novel nanopromoters by grafting hydrophilic groups (SO3−, COO− and N[CH3]3+) covalently on polystyrene nanospheres (Group@PSNS), and for the first time achieved rapid formation of methane hydrates together compact agglomeration by regulating the hydrophilic groups on the surface of nanopromoters. When SO3−@PSNS was used, methane hydrates formed rapidly but loosely in the reactor; while for COO−@PSNS and N(CH3)3+@PSNS, even the hydrate formation rate was seriously reduced, the formed hydrates agglomerated compactly in the reactor bottom. Interestingly, when both SO3− and COO− were fixed on the nanospheres, both the hydrate growth rate and agglomeration compactness were controlled. Especially, the nanopromoter with the SO3−/COO− molar ratio of 2:1 resulted in the formation of methane hydrates with compact agglomeration morphology within 1–2 hr and with the storage capacity reaching 140–145 vol/vol.