This paper studied the construction of Pear Diseases Domain Ontology (PDDO), and the realization of query system based on PDDO and SWRL. First, an approach to build PDDO based on SWRL was proposed, which consists of confirming core concepts, adding the properties of concepts and the relationships between concepts, adding the instances of concepts, representing domain ontology, adding SWRL rules and reasoning. Then the query system model and implementation algorithm were given. The query system, which integrates SWRL with Jess reasoning engine based on the SWRL rules, realized disease query, instance query, and diagnosis query by Protégé-OWL API. The query system realized excavating implicit relationships and renewing PDDO relative to previous system. Through the query system based on reasoning pear diseases knowledge can be obtained from PDDO according to user needs, furthermore, new and inferred knowledge are written to the PDDO owl file.