What Sun means here is that the freedom that people have should be subordinated to the needs of the country. He is saying that Western ideas about freedom put too much emphasis on people's ability to do what they want and not enough emphasis on the need of the society to be able to maintain its stability and coherence.
Sun talked about the idea that Chinese were like "loose sand" when they thought of freedom. They took it to mean that people should be able to do whatever they wanted. But Sun argued that there was the need for the state to have the power to force people to act in ways that would benefit the country as whole.
Sun argues that
Liberty, to put it simply, means the freedom to move about as one wishes within an organized group.
This shows what he means in the quote you have given. He means that individuals should have freedom, but that it should be limited. It should be limited by the boundaries that the state (the "organized group") puts on it.