The BRICS New Development Bank (NDB) and Asian Infrastructure Investment Bank(AIIB) are two new MDBs created by China and other emerging economies. Why do the NDB and AIIB take different operational institutions? NDB is taking a south-south cooperation operational institution, while AIIB’s operational modality is north–south cooperation. Based on the critical juncture theory of historical institutionalism, this paper, examines the different institutional proposals and the formation of multilateral proposal during the establishment negotiation processes of these two banks to explain the difference of operational institutions. In the establishment of NDB, India and China are competing for the leadership, making the principle of equality as the basic feature of the bank. All the founding members are borrowing countries. The NDB is a south-south cooperation MDB, equal shareholding and the use of country system as two prominent institutional innovations. In the establishment of AIIB, after the joining of the non-regional western powers, China is pushing AIIB in an internationalized and high standards approach with the political pressure of multilateralism especially from the European founding members and market pressure from the international credit rating agencies in the market, making it similar to existing MDBs in terms of operational institutions. This research shows the different approaches of emerging economies participating in the global economic governance system.