A microscopic geometry cutting device includes: a controller that outputs a timer count start command in starting a driving program which controls a drive of an X-axis or a Y-axis moving mechanism; an arrival time calculator that calculates an arrival time from when the timer count start command is output till when the cutter arrives at a machining start position in accordance with relative moving speed information of the moving mechanisms and machining start position information of a workpiece W; an elapsed time determiner that determines whether an elapsed time from when the timer count start command is output is coincident with the arrival time and outputs a trigger signal when the elapsed time is coincident with the arrival time; and a reciprocating stage driver that drives the reciprocating stage in a manner that the cutter advances and retracts in a predetermined cutting depth in response to the trigger signal.