The effects of the microstructure of conjugated polymer thin films on charge trapping and operational stability of organic field-effect transistors (OFETs) are investigated. Device characteristics of OFETs based on two model conjugated polymers, poly(3-hexylthiophene) (P3HT) and a random 3-hexylthiophene-thiophene copolymer (RP33), are compared. P3HT films have high crystallinity and long-range molecular order, whereas RP33 films have low crystallinity and short-range molecular order as well as enhanced polymer backbone planarity. Experimental evidence shows that although the microstructure of the RP33 film provides efficient charge transport pathways, its high degree of structural disorder causes severe shallow trapping of charge carriers, which results in its inferior stability under bias stress. This study demonstrates that low-crystalline conjugated polymers with short-range order can provide a high charge-carrier mobility but at the same time be inappropriate for practical OFETs because of their poor intrinsic operational stability.