The designer daughter of Sir Paul McCartney and mother-of-four was awarded Designer of the Year and Designer Brand of the Year at a star-studded event at London's Savoy hotel, the Daily Mail reported.
The double win follows a momentous year for McCartney, most notably her Team GB kit designs for the London 2012 Olympic Games.
Among the winners of the 14 other awards recognising talent across the fashion industry were Erdem, Nicholas Kirkwood, Roksanda Ilincic and JW Anderson.
Cara Delevingne was named Model of the Year, and Alexa Chung was once again given the British Style Award, which is voted by the public.
The winners at the British Fashion Awards are:
British Style brought to you by Vodafone - Alexa Chung
Outstanding Achievement in Fashion - Manolo Blahnik CBE
Emerging Talent Award (Ready-To-Wear) - J.W. Anderson
Emerging Talent Award (Accessories) - Sophie Hulme
Emerging Talent Award (Menswear) - Jonathan Saunders
Special Recognition - Harold Tillman CBE
Red Carpet Award - Roksanda Ilincic
Accessory Designer - Nicholas Kirkwood
Designer Brand - Stella McCartney
Isabella Blow Award for Fashion Creator - Louise Wilson OBE
New Establishment - Erdem
Model - Cara Delevingne
Menswear Designer - Kim Jones for Louis Vuitton
Designer of the Year - Stella McCartney