Writing on social media on Wednesday, Sheikh Mohamed said the messages have helped his family as they mourn the late president.
World leaders and dignitaries have travelled to Abu Dhabi in recent days to offer support.
"The heartfelt condolences of people from across the UAE and around the world have been a source of comfort to our family as we mourn the late Sheikh Khalifa," Sheikh Mohamed said.
"This response is a testament to his far-reaching impact and the respect that was felt for him both at home and abroad."
It follows a moving tribute that Sheikh Mohamed paid to Sheikh Khalifa on Tuesday.
“With his enduring wisdom and generosity, my brother, Khalifa bin Zayed, was the heart of our family and the guardian of our nation,” Sheikh Mohamed said.
“He was loved greatly and will be deeply missed, but his remarkable legacy will live on forever. May God grant him eternal peace.”