The rally on Saturday, organised by Chen Shui-bian, the Taiwanese president, marked the first anniversary of China's passage of the Anti-Secession Law that authorises war if Taiwan declares statehood, thereby violating Beijing's "one China" policy.
China and Taiwan split at the end of the Chinese civil war in 1949.
Chanting "Oppose missiles, Want peace", and holding red balloons and inflatable toy Chinese missiles, President Chen's Democratic Progressive Party (DPP) said the huge crowd showed to the world the Taiwan people's determination to defend a democratic way of life.
Song Wen-ling, 60, said: "Taiwan is not part of China and China should stop threatening us with its missiles and with its bullets."
Taipei said Beijing has accumulated nearly 800 missiles aimed at the island and was adding to its arsenal at a rate of between 75 and 100 a year.
Some security analysts say the Taiwan Strait is one of Asia's most dangerous spots.
Lee Guo-qing, a 48-year-old engineer, said: "Taiwan is a democracy, whether or not we should be independent or be part of China is up to us Taiwanese. We should not submit to China bullying."
Chen did not join the march to the presidential office. But in the speech at the end of the rally, Chen told the crowd that he stood firmly by his decision to scrap a symbolic Taiwanese body called the National Unification Council last month. His action was condemned by China.
Chen told the rally that China
could not decide Taiwan's fate
Chen said: "Taiwan is an independent, sovereign country. Taiwan's national sovereignty belongs to its 23 million people.
"Taiwan's national sovereignty, Taiwan's future is not up to China's 1.3 billion people to decide."
China relations favoured
For Taiwan's people, the issue of reunification versus independence has always been tricky. Opinion polls consistently indicate that more than 80% of Taiwanese prefer the status quo.
Last week, tens of thousands of opposition supporters, who favour closer ties with China, marched through Taipei to denounce Chen.