In this paper, we investigate the (two-sided) quaternion windowed linear canonical transform (QWLCT) and study the uncertainty principles associated with the QWLCT. Firstly, several important properties of the QWLCT such as bounded, shift, modulation, orthogonality relation, are presented based on the spectral representation of the quaternionic linear canonical transform (QLCT). Secondly, Pitt's inequality and Lieb inequality for the QWLCT are explored. Moreover, we study different kinds of uncertainty principles for the QWLCT, such as Logarithmic uncertainty principle, Entropic uncertainty principle, Lieb uncertainty principle and Donoho-Stark's uncertainty principle. Finally, we give a numerical example and a potential application in signal recovery by using Donoho-Stark's uncertainty principle associated with the QWLCT.