This paper proposes a checking method based on mutual instances and discusses three key problems in the method: how to deal with mistakes in the mutual instances and how to deal with too many or too few mutual instances. It provides the checking based on the weighted mutual instances considering fault tolerance, gives a way to partition the large-scale mutual instances, and proposes a process greatly reducing the manual annotation work to get more mutual instances. Intension annotation that improves the checking method is also discussed. The method is practical and effective to check subsumption relations between concept queries in different ontologies based on mutual instances.