Place sweet potatoes in a medium pot and cover with water. Bring sweet potatoes to a boil over high heat, then reduce heat to medium and simmer potatoes until very tender, about 15 minutes. Drain potatoes and transfer to a large bowl.
Whisk melted butter, maple syrup, cinnamon, nutmeg, milk, and vanilla until smooth. Mash sweet potatoes until smooth, then mash in butter mixture. Spread sweet potatoes in a greased 9x13 baking pan.
Make the apples: In a small saucepan over medium-high heat, saute apples in butter, sugar, and cinnamon until apples are just barely tender, about 5 minutes. Stir in pecans.
Spread apple mixture over top of sweet potatoes. Bake sweet potato casserole at 375F 15 minutes until heated through. Enjoy!