The main iSight camera is significantly improved, going from eight megapixels to 12 megapixels.
Meanwhile, the front-facing camera has also been optimised for selfies.
The screen now acts as 'flash', which varies in intensity depending on the light levels around you.
But the smart feature appears to have been lifted from popular apps, such as Snapchat, which do something similar.
The phones, which will be called the iPhone 6s and 6s Plus, start at £539 for the 16GB 6S model and £619 for the 16GB 6S Plus.
Earlier, Mr Cook showed off a new iPad line, saying: "Today we have the biggest news in iPad since the iPad."