Prabowo is making his first visit to a key trade partner of Jakarta since his victory in elections last month.
China is one of the biggest sources of foreign direct investment in Indonesia and has poured billions of dollars into projects in the archipelago nation.
Xi told Prabowo during talks in Beijing on Monday that bilateral ties "have entered a new stage of jointly building a community with a shared future", state broadcaster CCTV reported.
China "is willing to deepen all-round strategic cooperation with Indonesia and build a China-Indonesia community with... regional and global influence, so as to bring more benefits to the two peoples and make positive contributions to regional and world peace and development," Xi said.
Chinese companies have ploughed money into the extraction of Indonesian natural resources in recent years, particularly the nickel sector where Beijing's spending has stoked unrest over pay and working conditions.
Jakarta inaugurated Southeast Asia's first high-speed rail line last year, also a multi-billion-dollar project backed by Beijing.
Xi hailed the rail initiative as "a golden sign of high-quality cooperation between the two countries", according to CCTV.
The friendliness contrasts with Beijing's fraught ties with several other Southeast Asian nations -- particularly the Philippines -- over territorial claims in the disputed South China Sea.
Beijing claims the crucial waterway almost entirely and there have been repeated confrontations between Chinese and Philippine vessels around contested reefs in recent months.
Xi said the key to strong ties with Indonesia "lies in adhering to strategic independence, mutual trust and mutual assistance... and fairness and justice", CCTV reported.
"Both sides should... firmly support each other in safeguarding sovereignty, security, and development interests," he said.
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