But Li Keqiang added that his country would respect the choice of the Scottish people.
Premier Li joins a list of global leaders including American President Barack Obama, former US secretary of state Hillary Clinton and the Pope to have offered their views on independence in recent days.
In an apparent boost for the No campaign ahead of September's vote, he said he wanted a "strong, prosperous and united United Kingdom".
His comments will be of particular disappointment to Alex Salmond who has made a number of visits to China since becoming First Minister.
He added: "I believe that the United Kingdom can stay at the forefront in leading the world's growth and development and also continue to play an important and even bigger role for regional stability and global peace."
But he added: "We certainly respect the choice you make."
The pro-independence campaign Yes Scotland hit back, attacking the Communist superpower's record on democracy. A spokesman said: "Unlike people in China, people here will have a free and democratic vote on September 18 when they will decide on the future of their country. We believe that decision will be Yes."
Premier Li's comments, as he agreed £14 billion worth of trade and investment deals on his first official visit to the UK, appears to be a change of heart on the part of the Chinese administration.
Two years ago a state-run newspaper in the country urged China to back the SNP's independence campaign.
The paper argued that the move would send shockwaves through the Westminster Government, at a time when relations were still icy following a meeting between David Cameron and the Dalai Lama. The editorial in the Beijing-based Global Times said: "China cultivating more contacts with separatists in Northern Ireland and Scotland would make London quite uncomfortable. Perhaps it's time for Britain to change its way of thinking. Chinese now don't want to be bothered by such tough posturing."
Trade between the UK and China increased by eight per cent last year. Deals announced yesterday include an agreement worth £12 billion between BP to supply the China National Offshore Oil Company (CNOOC) with liquefied natural gas.
China Minsheng Investment Corporation (CMI), China's largest private sector investment group, also plans to open its European headquarters in London.
The Tory-Lib Dem Coalition was keen to use the visit to improve diplomatic and trade relations with China.
But there was controversy on the eve of the event when Deputy Prime Minister Nick Clegg appeared to praise the Dalai Lama, and suggested he would be honoured to meet the Tibetan spiritual leader, hated by Beijing, again.
Yesterday Mr Cameron said that part of his government's long-term economic plan was to link the UK to "the fastest growing economies on the planet and China is central to that".
l Former hostage Terry Waite has said Scottish independence would cause a "profound sense of loss".
Mr Waite, 75, held captive for almost five years in Lebanon as he tried to secure the release of British nationals, said that he had a "great affection" for Scotland.
"If (Scotland) was to separate, I would feel a profound sense of loss," he said as he gave a speech to mark 25 years of the Ayrshire Hospice.