The Real Presence of Jesus Christ in the Sacrament of the Eucharist: Basic Questions and Answers:
Why do we call the presence of Christ in the Eucharist a "mystery"?
The word "mystery" is commonly used to refer to something that escapes the full comprehension of the human mind. In the Bible, however, the word has a deeper and more specific meaning, for it refers to aspects of God's plan of salvation for humanity, which has already begun but will be completed only with the end of time.
In ancient Israel, through the Holy Spirit God revealed to the prophets some of the secrets of what he was going to accomplish for the salvation of his people (cf. Am 3:7; Is 21:28; Dan 2:27-45). Likewise, through the preaching and teaching of Jesus, the mystery of "the Kingdom of God" was being revealed to his disciples (Mk 4:11-12).
St. Paul explained that the mysteries of God may challenge our human understanding or may even seem to be foolishness, but their meaning is revealed to the People of God through Jesus Christ and the Holy Spirit (cf. 1 Cor 1:18-25, 2:6-10; Rom 16:25-27; Rev 10:7).
The Eucharist is a mystery because it participates in the mystery of Jesus Christ and God's plan to save humanity through Christ. We should not be surprised if there are aspects of the Eucharist that are not easy to understand, for God's plan for the world has repeatedly surpassed human expectations and human understanding (cf. Jn 6:60-66). For example, even the disciples did not at first understand that it was necessary for the Messiah to be put to death and then to rise from the dead (cf. Mk 8:31-33, 9:31-32, 10:32-34; Mt 16: 21-23, 17:22-23, 20:17-19; Lk 9:22, 9:43-45, 18:31-34).
Furthermore, any time that we are speaking of God we need to keep in mind that our human concepts never entirely grasp God. We must not try to limit God to our understanding, but allow our understanding to be stretched beyond its normal limitations by God's revelation. ^USCCB