"Cooperation with China is one of Russia's top priorities and it has reached an unprecedented level," Putin said.
Xi said the two countries have "always firmly taken the development of relations as a priority direction."
They have "resolutely supported the other's core interests ... and jointly proactively participated in international affairs and global governance," Xi said.
Following their talks, Xi presented Putin with China's newly created Friendship Medal at an elaborate ceremony.
The two leaders also signed a statement saying that "in conditions of a growing global instability and uncertainty" Russia and China will "deepen their consultations on strategic stability issues."
They vowed to "expand counter-terrorism cooperation," boost contacts between their militaries and encourage joint international efforts to fight terrorism "without any double standards."
The statement also criticized the U.S. decision to pull out of the Iran nuclear deal and said they would endeavor to keep it alive and ensure further trade with Iran.
Officials from the two nations signed a raft of agreements on cooperation in economic development, transport, space and nuclear energy.
They included deals envisaging the construction of two more nuclear reactors at China's Tianwan nuclear power plant and more reactors at another location.
An agreement was also reached for Russia to provide equipment and know-how for China to build an experimental fast neutron reactor.
Russia and China have responded to the U.S. national security strategy describing them as America's top adversaries by vowing to further expand their economic, political and military cooperation.
Putin has been driven closer to China by a sharp decline in relations with the West after Moscow's 2014 annexation of Crimea and support for a separatist insurgency in eastern Ukraine. Moscow is increasingly looking to Beijing for trade and investment following waves of Western sanctions targeting its vital energy sector and military industries and limiting the country's access to global financial markets.
China has come under growing criticism over its militarization of the South China Sea and accusations of unfair trading practices and human rights abuses.
Along with closer bilateral ties, they have also sought to strengthen the Shanghai Cooperation Organization, an eight-member regional grouping they created, which holds its annual summit in China this weekend.
Putin's visit comes just a month since he began his new term in office. He and Xi have met 25 times - five times last year alone, according to Putin's foreign affairs adviser, Yuri Ushakov.
Following a formal welcoming ceremony at the Great Hall of the People in central Beijing, Putin first with Premier Li Keqiang, telling him that Russia-China trade and economic ties have "gained a good tempo, and we are looking for new spheres of cooperation."
Li said bilateral trade is expected to reach $100 billion this year and voiced a readiness to expand cooperation in both traditional and new spheres, including nuclear energy.
Bilateral trade shrank from nearly $100 billion in 2014 to some $60 billion the following year due to a sharp depreciation of the Russian currency. It has since partly recovered as the ruble has strengthened, reaching nearly $90 billion last year.
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