A reciprocating ocean microstructure profiler includes a first profiler subunit, a second profiler subunit and a central stand. The first profiler subunit is provided with the first buoyancy drive part and the first observation part; and the second profiler subunit is provided with the second buoyancy drive part and the second observation part. Both the first and second buoyancy drive parts are installed with a floating compartment, a drive compartment and a pressure housing each. A top oil bladder is provided in the floating compartment and a bottom oil bladder in the pressure housing. A drive pump assembly and a solenoid valve are installed in the drive compartment. The first and second observation parts are electrically connected to a controller each and each controller is electrically connected to a drive pump assembly and a solenoid valve.