First Timothy 3:15 speaks of “the house of God, which is the church of the living God.” In the New Testament the house is also the household, the family, as in 1 Corinthians 1:16. The church is not a physical structure but a composition of all God’s New Testament people.
Likewise, New Jerusalem is not a physical city but the composition of God with all His Old and New Testament people.
In 1 Timothy 3:16 the church is involved in the mystery of godliness, God manifested in the flesh.* This manifestation is for today and will be greatly enlarged with New Jerusalem.
Today the manifestation is spiritual; when Christ returns the manifestation will be enlarged and much more evident. Colossians 3:4 speaks of this: “When Christ our life is manifested, then you also will be manifested with Him in glory.”
Today the church, as the manifestation of God in the flesh, is the house of God, whereas in the new heaven and new earth the New Jerusalem, as the manifestation of God in the new creation, will be the city of God. The city is much bigger than the house, signifying that the New Jerusalem, as the manifestation of God in His new creation, will be the enlargement and consummation of the church to express God in eternity.
As the old Jerusalem was the center and capital of God’s kingdom in the nation of Israel, the New Jerusalem will be the administrative center of the eternal kingdom of God in the new universe for the manifestation of God for the ages to come.**
* See Life-Study of 1 & 2 Timothy, Titus and Philemon, last half chap. 6, by Witness Lee
** Conclusion of the New Testament, The, chapter 13, by Witness Lee