The poet invites his beloved to look inside her heart, where a holy tree grows. Joy shakes its leaves. The shaking of the tree has made him murmur a wizard song for you.
The poet continues, telling his beloved not to look into the mirror, or only for a little while, because a dangerous image grows there. All things turn to barrenness and mirrors hold the image of out tiredness. In those frightening places the ravens of unresting thought fly, and make one's eyes unkind.
This poem, like many that are addressed to Maud Gonne, contrasts her inward with her outward beauty. On a simple level, the poem suggests that the beloved look within herself to the spirit of her nature (the tree), which he himself loves. Further, she should shun the mirror, which captures her external appearance. Her appearance, though beautiful now, will fade with age. Her inner tree, though, will never grow any less beautiful.
On a more arcane level, the holy tree could refer either to the tree of knowledge or to the Sephirotic tree of the Kabbalah. The Sephirotic tree resonates with both good and evil. This poem would fit with the Kabbalic notion of man, which is divided between good and evil. Looking in a glass makes the tree into its reverse image, barren and threatening. Yeats was certainly familiar with the Kabbalah from his theosophic practices.