Conjugated polymers containing non-aromatic cyclopentadiene (Cp) units have shown great application potential in high performance organic field effect transistors (OFETs). However, the relationship between the structure and properties of Cp-based polymers is underexplored, limiting further improvement of the OFET characteristics of these materials. Herein, we synthesized three copolymers of Cp and diketopyrrolopyrrole (DPP) units with side chains of different branching position and lengths PDPPCp-C4-OD, PDPPCp-C7-OD, and PDPPCp-C7-HO. It is found that the alkyl side chain structure has little effect on the thermal, optical, and electronic properties of the resulting polymers, but significantly influences the thin film microstructure. Among them, PDPPCp-C7-HO with a longer linear alkyl spacer as well as shorter branches adopted the most compact and ordered film microstructure, exhibiting the shortest π–π stacking distance, the largest lamellar coherence length and the highest degree of edge-on orientation in thin film after annealing at 200 °C. As a result, PDPPCp-C7-HO exhibited the highest hole mobility of 2.1 cm2 V−1 s−1 in OFET devices.