The visit, hailed by Patriarch Kirill as a "historic event", comes some three months before the presidential election in March in which Putin is widely expected to run and win a fourth term.
"We are seeing today how traditional values are being eroded in many countries, which leads to degradation, alienation in society, depersonalisation of people," Putin said in a speech to hundreds of top Russian Orthodox clerics from around the world.
"The state, while it respects the self-sufficiency and independence of the church, expects to continue our cooperation in such important spheres like education and healthcare, cultural and historical heritage, and helping families bring up youth," he said.
The congress of bishops is a top decision-making body of the Russian Orthodox Church, which convenes at least every four years and votes on key issues, including choosing the patriarch.
Most Russians consider themselves Orthodox, though few regularly practise.
The Russian Orthodox Church has given the Kremlin unwavering political support on issues ranging from Crimean annexation to involvement in Syria, even asking the clerics to help rebuild the war-wracked country.
"I expect the Russian Orthodox Church... to help the world community in the revival of Syria," Putin said at the congress.