The impact of thermal annealing on the growth of crystalline nanodomains of poly(3-alkylthiophene) (P3AT) in thin films (15-20 nm thick) was investigated as a function of length of alkyl side chain by combined low-dose high-resolution transmission electron microscopy (HR-TEM) and grazing incidence X-ray diffraction (GIXD). Statistical analysis of the data yields the characteristic dimensions of the face-on oriented P3AT nanocrystals, i.e., average stem length l(c) along backbones and lateral dimension perpendicular to the stems l(a) along side chains. The following trends were identified: (i) in as-spin-coated films, the proportion of face-on oriented nanocrystals increases with the number of carbon atoms in the side chain, (ii) annealing favors the lateral in-plane growth of the nanocrystals along the side chain direction (a(P3AT) axis), (iii) for a given P3AT, the proportion of face-on oriented domains increases with annealing temperature, (iv) lateral growth along the a(P3AT) axis is most efficient for the longer octyl side chains, and (v) thermal annealing induces only modest lamellar thickening which is limited by the poor slide diffusion of pi-stacked P3AT chains as opposed to lateral growth favored by weak van der Waals interactions between layers of n-alkyl side chains. The increase in the population of face-on oriented crystallites, observed when the length of the side chain increases, coincides with a corresponding decrease in the field effect mobility in annealed P3AT thin films.