Cyber-physical systems (CPSs) assisted by digital twins (DTs) integrate sensing-actuation loops over communication networks in various infrastructure services and applications. This study overviews the concept, methodology, and applications of the integrated communication quality estimation and control for the DT-assisted CPSs from both communications and control perspectives. The DT-assisted CPSs can be considered as networked control systems (NCSs) with virtual dynamic models of physical entities. A communication quality estimation observer (CQEO), which is an extended version of the communication disturbance observer (CDOB) utilized for time-delay compensation in NCSs, is proposed to estimate the integrated effects of the quality of services (QoS) and cyberattacks on the NCS applications. A path diversity technique with the CQEO is also proposed to achieve reliable NCSs. The proposed technique is applied to two kinds of NCSs: remote motor control and haptic communication systems. Moreover, results of the simulation on a haptic communication system show the effectiveness of the proposed approach. In the end, future research directions of the CQEO-based scheme are presented.