The manner in which both India and Bhutan stood together to address the situation in Dokalam "is a clear testimony to our friendship", a Rashtrapati Bhavan statement said.
Kovind, who met Bhutan King Jigme Khesar Namgyel Wangchuck, the queen and the prince at Rashtrapati Bhavan, said the security concerns of India and Bhutan are indivisible and mutual.
The president "conveyed deep appreciation for the King of Bhutans personal involvement and guidance and the support provided by Bhutan in addressing the recent situation in the Dokalam area", the statement said.
India and China's troops were locked in a 73-day stand- off in Dokalam, a tri-junction between Sino-India and Bhutanese border near Sikkim, from June 16 this year after Indian Army personnel stopped the Chinese Army from building a road in the disputed area.
The president said India and Bhutan share exemplary bilateral relations.
"Our relations are unique and special. Our bilateral ties are based on utmost trust and understanding. We should do everything to make it a model of bilateral cooperation, which will be noted by others in the neighbourhood," he said.
The president said India was delighted to see the rapid progress made in Bhutan while simultaneously preserving its very special culture as well as protecting the environment.
"India has been happy to share its knowledge, experience and resources with Bhutan. Our development cooperation has been guided by the priorities set by the government and people of Bhutan," he said.
Kovind also complimented the king of Bhutan on the successful completion of the first decade of his reign and his vision for a stable, happy and prosperous Bhutan.
The royal couple is on four-day visit to India.