In the Declaration of Independence, Jefferson claims that governments are instituted among men to secure the unalienable rights of Life, Liberty and the pursuit of Happiness. When a government fails to do that, it is the right and the duty of men to take it down and build a new one that does secure those rights.
In the overall argument, he is trying to prove that the English government has failed to fulfill its duties, so the thirteen colonies are entitled to break away from it and create its own government.