Shoigu's trip comes days after Xi spoke with his Russian counterpart Vladimir Putin, with the Chinese leader hailing Moscow's "positive efforts to defuse" the Ukraine crisis.
Speaking to Shoigu at Beijing's Great Hall of the People, Xi called China and Russia "friendly neighbours" and said the two sides would "maintain close communication at all levels", according to Xinhua.
Xi added that the countries would this year implement a "series of important agendas" for China-Russia ties.
China's foreign minister Wang Yi also attended the talks.
Moscow and Beijing have strengthened military and trade ties since Russia sent troops into Ukraine, though China has sought to depict itself as a neutral party amid the three-year conflict.
Beijing remains a close political and economic partner of Moscow and has never condemned Russia's actions, leading some NATO members to brand Beijing an "enabler" of the conflict.
Shoigu's visit -- his second to China in the past three months, according to Russian media -- comes after US President Donald Trump has pivoted towards Russia, sidelining Kyiv and European allies in a push for a deal to end the war in Ukraine.
Shoigu, Russia's former defence chief who is now secretary of the Security Council, held talks on Thursday with Malaysian Prime Minister Anwar Ibrahim in Kuala Lumpur.
The security chief -- seen as influential in the decision to send Russian troops into Ukraine in 2022 -- also met Indonesian President Prabowo Subianto and Defence Minister Sjafrie Sjamsoeddin in Jakarta this week.
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