Preheat your oven to 375°F (190°C). Grease a casserole dish with butter or non-stick spray.
Steam the sweet potato cubes until tender, which should take about 15 minutes.
In a large bowl, toss the steamed sweet potatoes with the sliced apples, maple syrup, thyme, cinnamon, nutmeg, salt, and melted butter.
Transfer the mixture to the prepared casserole dish, spreading it evenly.
For the topping, combine the pecans, brown sugar, flour, and a pinch of sea salt in a separate bowl. Add the cold butter cubes and mix until the mixture resembles coarse crumbs.
Sprinkle the pecan topping evenly over the sweet potato and apple mixture. Press down gently after each addition.
Bake in the preheated oven for 25-30 minutes, or until the topping is golden brown and the apples are tender. Allow the casserole to rest for about 10 minutes before serving.