Uncertainty is intrinsic in Cyber-Physical Systems since they interact with human and work with both analog and digital worlds. Since even minute deviation from the real values can make catastrophe in a safety-critical application, considering uncertainties in CPS behavior is essential. On the other side, time is a foundational aspect of Cyber-Physical Systems (CPS). Correct timing of system events is critical to optimize responsiveness to the environment, in terms of timeliness, accuracy, and precision in the knowledge, measurement, prediction, and control of CPS behavior. In order to design a more resilient and reliable CPS, first and foremost, there should be a way to specify the timing constraints that a constructed Cyber-Physical System must meet with considering existing uncertainties. Only then, we can seek systematic approaches to check if all timing constraints are being met, and develop correct-by-construction methodologies. In this regard, Timestamp Temporal Logic (TTL) is developed to specify the timing constraints on a distributed CPS. By TTL designers can specify the timing requirements that a CPS must satisfy in a succinct and intuitive manner and express the tolerable error as a part of the language. The proposed deduction system on TTL (TTL reasoning system) gives the ability to check the consistency among expresses system specifications and simplify them to be implemented on FPGA for run-time verification. Regarding CPS run-time verification, Timestamp-based Monitoring Approach(TMA) has been designed that can hook up to a CPS and take its timing specifications in TTL and verify if the timing constraints are being met with considering existing uncertainties in the system. TMA does not need to compute whether the constraint is being met at each and every instance of time but it re-evaluates constraint only when there is an event that can affect the outcome. This enables it to perform online timing monitoring of CPS for less computation and resources. Furthermore, the minimum design parameters of the timing CPS that are required to enable testing the timing of CPS are defined in this dissertation