A medical instrument holding apparatus includes a shaft slidably engaged into a housing and movable into and out of the housing, the housing includes a guiding member engaged with the shaft for guiding and limiting the shaft to slide relative to the housing only and for preventing the shaft from being rotated relative to the housing, a locking device is engaged onto the shaft and includes a positioning member for engaging with an anchoring member of the shaft and for locking the shaft and the housing together, and one or more fasteners are engaged with the housing and the locking device for securing the shaft and the housing together with the locking device.