A control shaft assembly for a manual transmission may include a control shaft that is reciprocated in a rectilinear direction and is rotated by a shift lever, a control finger unit that is mounted on one side of the control shaft and moves together with the control shaft and prevents dual engagement of gears while shifting, a guide body that is spaced apart from the control finger unit to be mounted on the control shaft and that guides shift positions of the control shaft, and a shift position detecting unit that is disposed between the other side of the control shaft and a transmission case and that detects shift positions while shifting up and down.