Compared to the widely studied classical coil−coil block copolymers (BCPs) with well-established phase diagram and recent advances achieved in all-conjugated diblock copolymers, the investigation into the phase behavior of all-conjugated triblock copolymers is rather limited. In this work, we prepare a series of triblock copolymers containing various poly(3-alkylthiophene)s (P3ATs), interrogate their phase transition between cocrystallization and microphase separation adjusted by a set of molecular parameters (alkyl side chains, block ratios, and block sequences), and correlate these different structures strongly to their optical properties. Poly(3-butylthiophene) (P3BT), poly(3-hexylthiophene) (P3HT), poly(3-(2′-ethyl)hexylthiophene) (P3EHT), poly(3octylthiophene) (P3OT), and poly(3-dodecylthiophene) (P3DDT) are selected, in which P3EHT has a much less crystalline capability than the other four components. Interestingly, when the P3EHT block is situated in the BCP middle position (P3BT-b-P3EHT-b-P3AT), a smaller side chain difference between the two outer P3BT and P3AT blocks and the P3EHT with a shorter main chain length favor cocrystallization in the triblock copolymers over microphase separation. Moreover, when changing the block sequence to place the P3EHT block at two terminals (P3OT-b-P3BT-b-P3EHT and P3BT-b-P3OT-b-P3EHT), they display stronger cocrystalline capability than P3BT-b-P3EHT-b-P3OT with the P3EHT in the central. At last, these various crystalline structures are related to their optical properties. This work demonstrates the tuning of the phase transition between cocrystalline and microphase-separated structures in conjugated triblock copolymers via molecular engineering, which correlate closely to their optical properties and may underpin their applications in optoelectronic devices.