Temporal information is pervasive and crucial in medical records and other clinical text, as it formulates the development process of medical conditions and is vital for clinical decision making. However, providing a holistic knowledge representation and reasoning framework for various time expressions in the clinical text is challenging. In order to capture complex temporal semantics in clinical text, we propose a novel Clinical Time Ontology (CTO) as an extension from OWL framework. More specifically, we identified eight time-related problems in clinical text and created 11 core temporal classes to conceptualize the fuzzy time, cyclic time, irregular time, negations and other complex aspects of clinical time. Then, we extended Allen's and TEO's temporal relations and defined the relation concept description between complex and simple time. Simultaneously, we provided a formulaic and graphical presentation of complex time and complex time relationships. We carried out empirical study on the expressiveness and usability of CTO using real-world healthcare datasets. Finally, experiment results demonstrate that CTO could faithfully represent and reason over 93% of the temporal expressions, and it can cover a wider range of time-related classes in clinical domain.