The combined effect of shear flow and ultrasound (US) waves on the dynamical structural orientations of cellulosic cholesteric liquid crystals was investigated by time-resolved, in situ small-angle X-ray scattering (SAXS). A dedicated channel-type shear flow/ultrasound cell for SAXS characterization was developed to simultaneously generate a shear flow-induced horizontal stress force and a US-induced vertical acoustic radiation force. The control of the alignment of anisometric cellulose nanocrystals (CNCs), with their director parallel to the ultrasonic wave direction of propagation, was revealed at an unprecedented nanometer scale. Concurrently, the application of shear flow induced a horizontal orientation of CNCs with their directors aligned along the velocity direction. By adjusting the level of simultaneously applied shear flow and US intensity to the CNC suspensions, it was possible to tune the direction and the level of orientation of the CNCs during a period of time. For a specific ratio of the applied shear rate to acoustic power, some transient orientation of the CNCs at an intermediate angle between horizontal and vertical directions was evidenced. Relaxation of these orientations’ phenomena upon cessation of flow and/or US was also highlighted.