Modi met Li at the Myanmar International Convention Centre on the sidelines of the back-to-back India-ASEAN and East Asia summits in Myanmar's capital.
Li was among the first leaders to have greeted Modi over phone after the latter was sworn in as Prime Minister in May this year. He had pledged then to build a "robust" relationship with Modi's government.
During the meeting, Modi recalled the visit of Chinese President Xi Jinping to India in September, saying it would be remembered as a memorable visit.
Li also said that China was looking forward to welcoming Modi.
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"Keen to have you visit China. Look forward to seeing you in Beijing," Li was quoted as saying by Ministry of External Affairs spokesman Syed Akbaruddin.
The Prime Minister met Li on a day when he had several bilateral meetings for the third day today during the course of his ten-day three-nation tour that will also take him to Australia and Fiji.
Modi met Russian Premier Dmitry Medvedev and Philippines President Benigno Aquino among other world leaders today.
Li is second-ranked in the Communist Party of China (CPC) after President Xi.
Modi will also have an opportunity to interact with President Xi during an informal meet of the leaders of the five-nation BRICS bloc on the fringes of the G-20 summit in Brisbane.
Modi and Xi are likely to enhance their rapport struck during their meetings at the BRICS summit in July in Brazil and during the President's visit to India in September.
National Security Advisor Ajit Doval also attended the meeting.