The LCMS operates under a congregational polity modified by synodical structure. Each congregation is self-governing and responsible for its own affairs, doctrinal purity, and discipline. However, congregations voluntarily join together in synods (regional and national assemblies) for mutual support, doctrinal accountability, and coordination of mission and education. The LCMS as a whole is governed by the convention (national assembly) that sets doctrinal standards and policies.

Scripture is the supreme authority in the LCMS (sola scriptura). The Lutheran confessions (Book of Concord) are acknowledged as faithful summaries and interpretations of Scripture, but they are subordinate to Scripture itself. No human authority—pope, church council, synod, or pastor—stands above Scripture or can contradict it with binding authority.

Apostolic succession (the doctrine that bishops in an unbroken chain back to the apostles possess special authority) is rejected in the LCMS. Instead, the LCMS teaches that the succession of doctrine (faithful transmission of the gospel) is what matters, not an unbroken chain of bishops. Pastoral authority is functional (the authority to teach, preach, administer sacraments, and discipline within the congregation) and flows from Scripture, not from special ontological status. The priesthood of all believers is affirmed; all Christians share in the priestly office of Christ, though not all are called to the pastoral office.