This invention discloses a scanning mechanism of an ion implanter. The mechanism is a PR-PRR type parallel mechanism with two subchains and two DOFs, driving the wafer holder to scan when the first subchain and the second subchain are translated in the same direction at the same speed and adjusting the rotational angle of the wafer holder when the first moving link (30) and the second moving link (32) in the first subchain and the second subchain have different translation amounts in the same direction or opposite directions. The driving motor for the scanning mechanism is provided outside the implant chamber. The invention also solves problems like low rigidity and large accumulation errors of existing serial scanning mechanisms and the effect of the electromagnetic field of the motor within the ion implant chamber on the trajectory of the ion beam.