In this paper, the exponential synchronization of stochastic complex networks without strong connectivity is discussed. Distinguished from the previous papers, we introduce a novel periodically intermittent control based on discrete-time state observations, instead of continuous-time state observations in the control time. The coupling structure of networks is time-varying. By employing the Kirchhoff’s Matrix Tree Theorem in graph theory and Tarjan’s algorithm, some sufficient conditions are derived. In particular, when the novel control degenerates into the feedback control based on discrete-time state observations, it is discussed in detail as well. Furthermore, we apply our main results to study the synchronization of stochastic coupled oscillators with time-varying coupling structure. Meanwhile, two synchronization criteria are derived. Finally, a numerical test is given to validate the effectiveness of our results.