To unveil the effect of canard’s vertical position (g/c_w=-0.15, -0.5,0, 0.05 and 0.15) on longitudinal aerodynamic characteristics of a dynamic canard configuration, both water-tunnel force measurements and CFD numerical simulations are conducted to research the unsteady pitching oscillations (k=0.037 5 and 0.600 0) of canard configurations. It has been found that the variations of canard’s vertical position bring more influences on the lift coefficients of the canard than the ones of wing. During the low-frequency pitching-up process, the canard vortex of the lower deployed case becomes more sensitive to the interaction from the downstream wing, which brings an earlier double-spiral breakdown of canard vortex. When undergoing the low-frequency pitching-down process, the canard vortex of the lower deployed case is harder to rebuild than the higher deployed one. During the high-frequency upstroke process, due to the large reduction of canard leading-edge effective attack angle, the canard vortex initially develops on the lower surface of the canard for both lower and higher deployed cases. When undergoing the high-frequency downstroke process, the convection flow of canard vortex for the lower deployed case is faster than the higher deployed one, thus the canard lift coefficients of the former case become smaller. In addition, compared to the canard configuration with a lower deployed canard, the higher deployed case can own a larger maximum lift coefficient of wing during the low frequency pitching oscillations. When undergoing a high-frequency downstroke stage, due to the breakdown of wing vortex and canard’s vertical position, the wing lift coefficients of the higher deployed case become smaller.