A series of poly(3-hexylthiophene)-block-polyisoprene (P3HT-b-PI) diblock copolymers (DBCP) and polyisoprene-block-poly(3-hexylthiophene)-block-polyisoprene (PI-b-P3HT-b-PI) triblock copolymers (TBCP) with accurately controlled molecular architecture were synthesized via highly efficient coupling reaction between aldehyde end-functionalized P3HT and living anionic polyisoprene. The self-assembly behaviors, considering morphology and crystallinity, of the thermal annealed bulk samples of these DBCPs and TBCPs containing various PI content were systematically investigated. The DBCPs behaved very differently from most published P3HT BCP systems, showing elongated fibers with preserved crystallinity regardless of the PI fraction. More noteworthy, with PI fraction less than 40 wt %, the DBCPs exhibited parallel straight fibers longer than several micrometers accompanied by concurrent enhanced crystallinity. The unique microstructure of the DBCPs might originate from moderate microphase separation between P3HT and PI as well as high flexibility of PI to conduct the packing of P3HT. The TBCPs, by contrast, exhibited highly curved interdomain boundaries with significant depressed crystallinity, resembling P3HT diblock copolymers in the strong phase segregation regime, as more pronounced entanglement of the two terminal PI segments would restrict the movement of P3HT.