In the narrow orifice of a cone-shaped channel, blockage can occur for granular matter. However, water molecules can enter into and even permeate through carbon nanotubes of diameters down to 0.8 nm at ultrafast rates. Here we demonstrate by molecular dynamics simulations that clogging can also emerge unexpectedly in the water flowing through a nanoscale valve-less pump. The designed pump features two truncated carbon nanocones, with the narrowest region having a diameter of 1.2 nm (larger than that of (6, 6) carbon nanotube), linked to a fluid cavity volume, and is powered by the vibration of a graphene sheet. In the low frequency range, water molecules can be driven through the nanocones effectively by the vibration of the graphene sheet. The maximum flux reaches 83 ns ^–1, which is approximately 20 times the measured value of (3.9 ± 0.6) ns ^–1for aquaporin-1. However, at higher frequencies, water molecules suffer blockage at the narrow exits. Much unlike granular matter, high-frequency vibration cannot restore water flow. The key to this phenomenon is that in the narrow exits of two nanocones acting as diffuser/nozzle, the number density of water molecules rapidly increases with frequency increasing, the tight hydrogen-bonding network is formed, and the mean lifetime of hydrogen bonds increases dramatically under high-frequency vibrations. High frequency fluctuations in the middle chamber make H-bond network between water molecules in the narrow exits more stable. The probability density distribution of water exhibits a non-equilibrium transition from a disordered state to ordered state. This work reveals a new mechanism of water flowing/blocking in a nanoscale valve-less pump based on two asymmetrical nanocones, offers valuable insights into understanding nonequilibrium jamming transition in nanoscale fluid.