The light-harvesting complex of photosystem II (LHCII) plays the dual roles of photosynthetic energy capture and dissipation, where the excitation energy in excess is dissipated safely via non-photochemical quenching (NPQ) to avoid photodamage. Chlorophyll excimer was recently reported to be an intrinsic photophysical intermediate in LHCII, which may serve as an efficient quencher of Chl singlet excitation (1Chl*). We have employed ultrafast transient absorption and broadband two-dimensional electronic spectroscopy to investigate the mechanism of 1Chl* deactivation in quenched and non-quenched LHCII preparations, referred to as Q-F730 and U-F680, respectively. It is found that the photoproduction of carotenoid (Car) triplet excitation in Q-F730 is substantially lower than that in U-F680, implying that intersystem crossing is unlikely to be the major deactivation channel of 1Chl*. In addition to the Chl-to-Car singlet excitation transfer pathway, our data are consistent with 1Chl deactivation via the formation of a Chl excimer and subsequent population of a Chl charge transfer state. Our spectroscopic results provide direct evidence linking the excimer to the Chl singlet excitation in LHCII, shedding light on the mechanistic basis of NPQ.