On Tuesday, Lien was given a red-carpet welcome by the head of the Communist Party's Taiwan office, Chen Yunlin, and leaders of the state council's Taiwan affairs office as well as leading party officials from Jiangsu province.
It is the first visit by a Kuomintang (KMT) Party chairman to mainland China since it lost a civil war to the communists and fled to Taiwan in 1949.
Lien said he was honoured and happy, and would cherish his time in China, which considers Taiwan part of its territory awaiting reunification by force, if necessary.
He said he would use the visit to improve relations across the Taiwan Straits.
"Concerning the common future of the two sides of the straits and how we can reach a future of mutual benefit and a peaceful win-win situation, it is an issue that everyone is concerned about," Lien said at the airport.
"The delegation of the Kuomintang hopes to reach the goal of a peaceful and stable cross-strait relationship and we will work towards this"
Taiwanese opposition leader
"The delegation of the Kuomintang hopes to reach the goal of a peaceful and stable cross-strait relationship and we will work towards this. We really hope people from all walks of life ... will also strive for this."
Because there have been no regular direct flights between China and Taiwan since they split in 1949, Lien and his 70-strong KMT delegation arrived in Nanjing, China's capital when the KMT was in power, from Hong Kong.
As Lien left Taipei, hundreds of pro-independence protesters opposed to the visit clashed with his supporters inside the airport.
Several hundred broke into the departure hall and clashed with up to 100 of Lien's supporters, throwing eggs and stones.
opposed Lien's visit to China
Some wrestled with each other while others fought with sticks and let off firecrackers. Several people were injured including at least two men, whose heads were covered in blood.
Hundreds of baton-wielding riot police jostled with crowds inside the airport terminal in an attempt to keep the two sides apart. Many more protesters from both sides gathered outside the airport building.
Government supporters, angry over the KMT's engagement with Beijing, held up placards saying "Lien Chan is selling Taiwan" and "Lien Chan get out".
Lien is due to meet President Hu Jintao in Beijing on Friday during his controversial eight-day "peace journey", which will also take him to his birthplace, Xian, and the commercial centre of Shanghai.
It will be the first meeting between the heads of the KMT and the communists since Mao Zedong met Chiang Kai-Shek in Chongqing in 1945 to negotiate an end to the civil war.
Hu Jintao (above) will meet Lien
for peace talks on Friday
Analysts said Beijing would use the visit to woo Taiwanese people and remind them of the benefits of accepting China's stance that the island belonged to the mainland and should be reunified with it.
Taiwan's independence-leaning President Chen Shui-bian has reversed his earlier criticism of the trip, reportedly under pressure from Washington.
But the decision-making body of Taiwan's China policy, the Mainland Affairs Council, on Monday warned Lien not to risk breaking the law by engaging in state-related negotiations or signing agreements with Beijing.
Lien has urged the two sides to re-open dialogue to settle sovereignty disputes dating back to the civil war.
Beijing called off the last round of talks in 1995 after an unprecedented US visit by Taiwan's then president Lee Teng-hui.
Tension between China and Taiwan has been high since China's parliament in March adopted an anti-secession law giving its military the legal basis to attack Taiwan if the island moves towards formal independence.
Ties between the two were already strained after Chen, from the Democratic Progressive Party (DPP), broke the KMT's 51-year grip on power in the 2000 presidential election. He was re-elected in 2004.