In this paper, the quasi-synchronization problem of heterogeneous stochastic coupled neural networks (HSCNNs) is discussed. The effects of the mixed time-varying delay and diffusion phenomenon on the system are considered separately in time and space. Moreover, different from the previous distributed control, boundary control is introduced to realize network synchronization. This not only reduces the space cost of the controller, but also makes it easier to implement. Thus, the mean-square quasi-synchronization of HSCNNs is guaranteed by using matrix inequality and stochastic analysis tools. In addition to focusing on systems with Neumann boundary conditions, we briefly investigate HSCNNs with time-invariant delays and mixed boundary conditions respectively, and provide sufficient conditions to achieve the desired performance. Finally, the correctness of the conclusion is verified by several examples.