Ms Sitharaman, who arrived in Beijing yesterday, attended the SCO defence ministers' meeting today.
During her meeting with General Wei Fenghe, Ms Sitharaman said that differences should not lead to disputes in relations between India and China, officials said.
In August last year, India and China ended their 73-day standoff between their troops in Doklam. The standoff had strained ties considerably between the two countries.
The annual summit of the SCO, in which India is the latest entrant along with Pakistan, will take place in the Chinese city of Qingdao in June.
The SCO, headquartered in Beijing, was founded in 2001.
Comprising China, Russia, Kazakhstan, Uzbekistan, Tajikistan, Kyrgyzstan, India and Pakistan, the SCO aims at military cooperation between the member states and involves intelligence sharing, counter-terrorism operations in Central Asia and joint work against cyber terrorism.
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