Translation:She is going to think that I do not love her.
I was thinking this too, and was looking in the comments to see if it came up before posting, and sure enough it came up! I put "She is going to think that I do not want her" and was marked correct. Amore means to love, whereas quiere means to want. Note that many people use the word love (probably not just in Spanish and English) when most of the time it really doesn't deserve the name of love, and is desire.
Well when it's a sentence alone like this, you just can't talk about something that is not there, but let's say it's a conversation:
María: ¿Usaste la bicicleta que te regaló Carla? Juan: No, voy a tener que usarla porque si no ella pensará (va a pensar) que no la quiero.
In a case like that yes it can be "She is going to think that I don't want it." cause he is not mentioning the bike, but he IS talking about it.
María: Did you use the bicycle Carla gave you? Juan: No, I'm going to have to use it, if not she is going to think that I do not want it.
You have a mistake:
She is going to think that I don't want it -> is for an object:: Ella va a pensar que yo no lo quiero
She is going to think that I don't want him -> is for a male person: Ella va a pensar que yo no lo quiero (As with an object)
She is going to think that I don't want her -> is for a female person: Ella va a pensar que yo no la quiero
have a look to this other thread
You should listen to the slow version too because she articulates each word. In Spanish speech, when the final letter of a word and the beginning letter of the following word would be diphthong if used within one word, you sound the letters as a diphthong even though they are in separate words. If it happens to be the same letter repeated, then, as droma pointed out, the letter sound just becomes slightly longer.