The interest rate for the one-year facility was raised to 3.30 percent from 3.25 percent, the People's Bank of China said in a statement on its website.
The central bank lent 367.5 billion yuan ($58.54 billion) to financial institutions on Tuesday via the bond instrument, according to the statement.
The PBOC did not inject any fresh funds via the liquidity tool as same amount of MLF loan is set to expire on Tuesday.
The PBOC said in the same statement that it skipped reverse repos on Tuesday morning.
China's central bank raised the seven-day rate in March, following the US Federal Reserve Bank's March 21 move, seen by markets as a symbolic reminder that Beijing is keeping an eye on global market developments. The PBOC adjusted the rates on 14-day tenor on Monday.