The president greeted China and its people on the country's 65th foundation day Oct 1.
In a message of felicitation to his counterpart Xi Jinping, Mukherjee said: "As two of the most significant emerging economies, deeper engagement between our two countries is in the interest of Asia and the international community."
He termed President Xi's recent visit to India as an "important landmark" in the development of strategic and cooperative partnership for peace and prosperity between the two countries.
"Our discussions during the visit further underscored the global and strategic dimensions of our relations and highlighted the need for constructive and candid dialogue between us at all levels," Mukherjee said.
"Our mutual agreement to establish a closer developmental partnership reached during your visit will give a further boost to our economic and people-to-people exchanges, which, I believe, will provide a sound basis for enhancing and deepening our bilateral ties," he added.
"Please accept, Excellency, my best wishes for your good health and for the continued prosperity and well-being of the people of China," he said.