The properties of quark gluon plasma (QGP) have been investigated in heavy ion collision experiments. There, the suppression of quarkonium yield is regarded as a good probe for the screening of color charges in the QGP. Since the experimental data of quarkonium reflect its entire evolution in the QGP, it is important to develop our understanding of the in-medium evolution of quarkonium. We discuss the dynamics of quarkonium by applying the methods of open quantum systems. In this framework, information of the system is given by a density matrix, whose evolution is described by the master equation. Recently the effects of quantum dissipation on the dynamics have been discussed and its importance has been shown [1,2]. In this talk, we derive the master equation in the Lindblad form for the relative motion of a quarkonium. We solve the Lindblad equation by quantum state diffusion method and discuss how the dissipation and the color singlet-octet transitions affect quarkonium equilibration process. [1] Akamatsu et.al, Quantum dissipation of a heavy quark from a nonlinear stochastic Schrodinger equation,arXiv:1805.00167,JHEP07(2018)029 [2] Miura et.al, Quantum Brownian motion of a heavy quark pair in the quark-gluon plasma,arXiv:1908.06293,Phys. Rev. D 101, 034011