The Kuala Lumpur-Beijing service -- formerly MH 370 -- will now take on the code MH 318, while the return route will switch from MH 371 to MH 319.
"As a mark of respect to the passengers and crew of MH 370 on 8 March 2014, the MH 370 and MH 371 flight codes will be retired," the national carrier said in a statement.
The airline said the changes would take effect from tomorrow.
"There are no changes to the frequency of our services, and we will continue to operate double daily services to Beijing," the airline added.
"Our thoughts and prayers remain with the families of our colleagues and passengers of MH370."
The search for the Boeing 777 entered its sixth day today with Chinese satellite images showing possible debris in the South China Sea -- but Vietnamese planes found no trace of the objects, an official said.
The search for the missing airliner now encompasses an area of more than 90,000 square kilometres -- roughly the size of Portugal.
Theories about the possible cause of the disappearance range from a catastrophic technical failure to a mid-air explosion, hijacking or even pilot suicide.