Misaki no Mayoiga

The setup is very similar. Our main character(s) moved to a new place due to circumstances outside of their control and much of the story details how they adjust to their new life. "Misaki no Mayoiga" is what you get if you combine "In This Corner of the World" with the supernatural elements of the type present in "Okko's Inn" 

Both films utilize supernatural elements and beautiful visuals to examine themes of growing up, trauma, family, and home in family-friendly yet mature stories. 

Elements of magic. Easy going home life depicted that warms the soul. It isnt similar in that the main characters in Flying Witch aren't necessarily coming from a rough background. But the main character is going to stay at a relative's place, finding shelter on her journey. How it's mainly similar is how the elements of magic and spirits of nature are presented in a matter of fact & realistic form. ALso; flying witch has a clean cut, yet intuitive and high quality plot episode to episode, similar to the well told story of Mayoiga