"Never in history has someone who persecuted those with upright faiths ever succeeded," said Li's message, describing China's 20-month campaign against the spiritual movement as "futile".
The message posted on Falun Gong Websites is Li's first major statement since five people China says were Falun Gong practitioners set themselves on fire in Tiananmen Square on January 23.
Appearing to refer throughout the text to the Chinese leadership as "the evil", Li said the torture and beating of his followers would turn the entire population against the Communist Party.
"The evil's persecution in China -- which ignores all of its consequences -- will lead people to completely distrust the ruling party and its regime, and to disobey the government," it said.
China's onslaught against the spiritual movement, which was banned in July 1999 as an "evil cult", has been stepped up another gear since the mass suicide attempt with arrests and a strident propaganda campaign.
Speaking at the opening of the China's parliament in Beijing on Monday, Premier Zhu Rongji vowed there would be no let-up in the crackdown.
"We need to continue our campaign against the Falungong cult, and further expose and condemn the anti-human, anti-social and anti-science nature of the cult," Zhu said.
Li, who lives in exile in New York, said the crackdown had been carried out using the "most base actions ever in human history".
"Although many people have been beaten to death, beaten to disability or sent to mental hospitals, this has not changed true cultivators' righteous thoughts," said Li.
And he said those Falun Gong followers who have renounced their beliefs under torture or pressure were still part of his movement.
"When they return to their senses, they will immediately start doing what a Dafa (Falun Gong) student should do and in the meantime will declare null and void everything they said and wrote when they were not in their right minds."
Hong Kong Falun Gong spokeswoman Sophie Xiao said the message was Li's most important since his "Beyond Limits of Forbearance" of January 1, which China says encouraged followers to commit suicide.
Falun Gong, which combines Li's Buddhist- and Taoist-based philosophy with slow-motion meditation exercises, has always insisted the five people who set themselves on fire in Tiananmen Square were not members of the movement.
Xiao said Li's new statement was a message to practitioners to do what they think is right but was not necessarily encouraging them to make new protests.
She added: "He is not only talking about practitioners here, he is talking about ordinary people. The more people see the paranoid actions of the government, the more they will understand who is right and who is wrong."
Since the movement was banned tens of thousands of followers have flocked to Tiananmen Square to make almost daily protests. The movement claims 70 million members in China, although Beijing says it only ever had two million.