We have to get almost to the end of the book in order to figure out what the title, A Mango-Shaped Space, means. After Mia gets back from the synesthesia event, she tells us:
As if on cue, a flash of lightning shows me that Mango is definitely not on the bed. The only thing there is a Mango-shaped space. (13.56)
Go on and break our hearts, why don't you? Mia's bed is empty and her beloved cat dies pretty soon after this, leaving Mia feeling empty and angry inside. The fact that the title comes to us from this section of the book makes us focus on the space that Mango leaves in Mia's life after he dies. For a girl who's just started to come into her own and be herself in all her quirky glory, Mango has been a true source of comfort along the way. And now he's gone. Tear.