Nanoconfinement of conjugated polymers (CPs) is an effective strategy to control the orientations and orderings of CPs, which determine their electrical properties. We investigate the chain orientations of two crystal polymorphs, Form I and Form II, in poly(3-dodecylthiophene)s (P3DDTs) using a porous anodic aluminum oxide (AAO) template. The control of regioregularity (RR) of P3DDTs results in well-defined Form II/Form I ratios of crystal polymorphs. Interestingly, Form I and Form II crystals show considerably different orientational changes depending on the pore diameter (Dpore) of the porous AAO template. As Dpore decreases from 100 to 30 nm, Form II crystals change their orientations from face-on to edge-on dominant morphologies, whereas Form I crystals consistently exhibit edge-on dominant morphologies. In addition, for a fixed Dpore of 100 nm, temperature-dependent orientational changes of Form I and Form II are investigated. While Form II crystals show a significant orientational change with increasing temperature, Form I crystals only experience chain reconfiguration. This finding provides useful guidelines for achieving the CPs with controlled intermolecular assembly and chain orientations.