To harness the abundant water flow energy for powering remote sensors or small microelectronic systems in the ocean is of great significance. Piezoelectric energy harvesting from flow induced motion can be an approach. In this paper, a piezoelectric energy harvester was embedded in a cylinder to form an inertial energy harvester. The cylinder together with springs forms a two-degree-of-freedom vortex induced motion structure in the flowing water. Two downstream columns were placed near the cylinder in the in-line direction, which can produce collisions between the column and the cylinder and offer a frequency up-conversion mechanism for the inside piezoelectric energy harvester. The system is analyzed theoretically based on the fluid mechanics and a prototype is fabricated for verification. Experiments were conducted in a low-speed circulating water channel. The trajectory of the cylinder was experimentally investigated. It is demonstrated that the output performance of the energy harvester is related to the flow speed and the gap distance between the columns and cylinder. The results show that when the flow speed is 0.371 m/s and the gap distance is 17 cm, the maximum output of the energy harvester is 861.39 μW for one piezoelectric element with a 150 kΩ external resistor.