The organisation of TOP 09 is four-tiered:
- The nationwide organisation encompasses all regional chapters.
- Regional organization acts within the boundaries of the region and consists of all local and county organisations of the Party in the territory of the respective region.
- County organisation acts usually within the county boundaries. In regions with a lower number of members, one county organisation may act on behalf of several neighbouring counties. The county organisation consists of all local organisations and party members in the given territory.
- A local organisation is the basic organisational unit of the Party. It may be founded in communities with at least 3 party members. A local chapter may act in the territory of more communities provided the requirements of the minimum number of 3 party members and their belonging to the same county chapter are satisfied. County organisations also carry out the tasks of local organisations in communities where no local organisation is active.
The National Assembly is the highest TOP 09 authority. Its participants are members of the Executive Committee and delegates selected at Regional Conferences. The National Assembly takes place every two years and it primarily elects the Chairman of TOP 09, Vice-Chairman, members of the Presidency and members of the Executive Committee.
The Executive Committee is the Party's executive body. It convenes as needed, at least once every two months and its voting members are members of the Party Presidency, fourteen members elected at the National Assembly, and then Government members, Deputies and Senators of the Czech Houses of Parliament, Members of the European Parliament and Regional Governors who are Party members.
The Executive Committee approves the annual budget draft and the annual financial reports, discusses crucial political issues, submits, on behalf of the Party, proposals for appointments at the national level, decides on the final ranking of candidates on the Party list for elections to the Chamber of Deputies, decides on the nomination of candidates for individual election districts for the Senate elections, and forges election and post-election coalitions and so on.
The Party Presidency is an operative executive body. It consists of the Honorary Chairman, the Chairman, the First Vice-Chairman, up to four Vice-Chairmen, the Chairman of the Fraction in the Chamber of Deputies and in the Senate and the Faction of Members of the European Parliament and up to five members of the Party Presidency.