According to the Prime Minister's website, both the leaders held discussions regarding enhancing bilateral ties during the sidelines of the G20 summit here.
"Another bilateral follows first session at G20. PM meets Mohammad bin Salman, Deputy Crown Prince of Saudi Arabia," External Affairs Ministry spokesperson Vikas Swarup tweeted soon after the meeting.
Mohammad, who is the son of Saudi King Salman, also holds the key defence and economic policy portfolios of the oil-rich Gulf Kingdom.
Modi earlier met US President Barack Obama briefly when they were on a stage to pose for a family photograph at the venue in this eastern Chinese city.
He will meet his British counterpart Theresa May and Argentinian President Mauricio Macri on Monday before returning to Delhi.