The present invention relates to a benzodithiophene based copolymer containing isoindoline-1,3-diketone units and a preparing method and applications thereof. The polymer has a structural formula (I), wherein R1 and R2 are respectively selected from H or alkyl groups of C1 to C16; R3 and R4 are respectively selected from H, alkyl groups of C1 to C16, alkoxy groups of C1 to C16, or thiophene groups substituted by alkyl groups of C1 to C16; R5 is selected from alkyl groups of C1 to C16; n is a natural number from 7 to 80. Applications of the benzodithiophene based copolymer containing isoindoline-1,3-diketone units in polymer solar cells, polymer organic light-emitting, polymer organic field effect transistors, polymer organic optical storage, polymer organic nonlinear materials or polymer organic laser are also provided.