With the tremendous development in size, the complexity of ontology increases. Thus ontology evaluation becomes extremely important for developers to determine the fundamental characteristics of ontologies in order to improve the quality, estimate cost and reduce future maintenance. Our research examines the concepts and their hierarchy in conceptual model, the common feature of the most ontologies, which reflects the fundamental complexity. We suggest a well-defined metrics suite of complexity, which mainly examine the quantity, ratio and correlativity of concepts and relationships, to evaluate ontologies from the viewpoint of complexity and its evolution. In the study, we measure three ontologies in GO to verify our metrics. The results indicate that this metrics suite works well, and the biological process ontology is the most complex one from the view of complexity, and the molecular function ontology is the unsteadiest one from the view of evolution.