SummaryThe synchronization problem of linear over‐actuated multi‐agent systems with unmeasurable states is studied in this paper, under both limited communication data rate and switching topology flows. A class of adaptive quantized observer‐based encoding–decoding schemes and a class of certainty equivalence principle‐based control protocols are proposed. By developing the graph‐based space decomposition technique and analyzing the closed‐loop quantized dynamic equations, it is shown that if the network topology flow is jointly connected, the communication channels are periodic active, and the agent dynamics is observable, and with the orthogonal system matrix, the proposed communication and control protocols can ensure the closed‐loop system to achieve synchronization exponentially fast with finite bits of information exchange per step. Copyright © 2015 John Wiley & Sons, Ltd.