The two shook hands outside the Great Hall of the People and inspected an honour guard as Thein Sein -- a former general -- was given full military honours.
Xi noted the four-day trip is Thein Sein's fifth visit to China and third official journey.
"This fully demonstrates the importance you place on developing China-Myanmar relations," Xi said.
Beijing was a traditional supporter of Myanmar for decades when the resource-rich Southeast Asian country was diplomatically isolated as human rights suffered under military rule.
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China in turn had access to Myanmar's abundant natural resources such as metals, timber and gemstones, as well as involvement in numerous hydropower projects.
But in 2011 Myanmar's junta handed power to a quasi-civilian government. It launched dramatic political reforms that helped to sweep away most Western sanctions.
As a result the relationship with Beijing has changed, and the key Chinese-backed Myitsone dam project was suspended.
In May, two Chinese workers kidnapped and threatened at a China-backed copper mine in Myanmar were released after being held by activists demanding a halt to the project.
The 1954 Five Principles of Peaceful Coexistence include mutually respecting sovereignty and territorial integrity as well as mutual non-aggression and mutual non-interference in domestic affairs.