In this paper, we investigate the asymptotical consensus tracking problems for multiple-input-multiple-output (MIMO) linear multi-agent systems (MASs) with directed switching topology and a non-autonomous leader subject to nonzero unknown inputs. First, we design a full order unknown input observer (UIO) based on relative outputs to estimate the relative full states. Based on this UIO, we design a continuous consensus controller by introducing a decay function which remains positive into the term that is used to eliminate the effects of leader's nonzero inputs. And by using the multiple Lyapunov functions (MLFs) method, we prove that asymptotical consensus can be achieved if the average dwell time (ADT) is greater than a positive threshold. Second, we design a continuous consensus controller based on a reduced order UIO that can significantly simplify calculations. Finally, we give two examples about multiple unmanned aerial vehicles (UAVs) to verify the theoretical results. Compared with existing works, the continuous controllers here can not only achieve zero error consensus tracking, but also are chattering free.