Walden Two's title is a direct reference to Henry David Thoreau's book Walden. In the novel, the Walden Community is mentioned as having the benefits of living in a place like Thoreau's Walden, but "with company". It is, as the book says, 'Walden for two' - meaning a place for achieving personal self-actualization, but within a vibrant community, rather than in a place of solitude. Originally, Skinner indicated that he wanted to title it The Sun is but a Morning Star, a quote of the last sentence of Thoreau's Walden, but the publishers suggested the current title as an alternative.
In theory and in practice, Thoreau's Walden experiment and the fictive Walden Two experiment were far different from one another. For instance, Thoreau's Walden espouses the virtues of self-reliance at the individual level, while Walden Two espouses (1) the virtues of self-reliance at the community level, and (2) Skinner's underlying premise that free will of the individual is weak compared to how environmental conditions shape behavior.
The cover of Walden Two, shown above, includes an "O" filled with yellow ink, with yellow lines radiating from the center of the "O". That Sun-like "O" is an allusion to the proposition that "The sun is but a morning star".