Disclosed herein is method and a navigation system for dynamically controlling navigation of an autonomous vehicle. In an embodiment, method comprises determining a trajectory path, comprising a plurality of path segments including at least one curved path segment and a straight path segment, by adjusting a plurality of waypoints in a base route of the autonomous vehicle and joining the plurality of waypoints using a predefined path planning model. Thereafter, a velocity profile distribution is generated for the autonomous vehicle by determining a start terminal velocity, an end terminal velocity and acceleration of the autonomous vehicle through each of the plurality of path segments in the trajectory path. Finally, a dynamic motion command is determined and applied to the autonomous vehicle based on the velocity profile distribution for dynamically controlling the navigation of the autonomous vehicle.