This paper proposes a system identification algorithm for systems with multi-rate sensors in a discrete-time framework. It is challenging to obtain an accurate mathematical model when the ratios of inputs and outputs are different in the system. A cyclic reformulation-based model for multi-rate systems is formulated, and the multi-rate system can be reduced to a linear time-invariant system to derive the model under the multi-rate sensing environment. The proposed algorithm integrates a cyclic reformulation with a state coordinate transformation of the cycled system to enable precise identification of systems under the multi-rate sensing environment. The effectiveness of the proposed system identification method is demonstrated using numerical simulations.