Thermoelectric (TE) materials have been considered as a promising energy harvesting technology for sustainably providing power to electronic devices. In particular, organic-based TE materials that consist of conducting polymers and carbon nanofillers make a large variety of applications. In this work, we develop organic TE nanocomposites via successive spraying of intrinsically conductive polymers such as polyaniline (PANi) and poly(3,4-ethylenedioxy- thiophene):poly(styrenesulfonate) (PEDOT:PSS) and carbon nanofillers, and single-walled carbon nanotubes (SWNT). It is found that the growth rate of the layer-by-layer (LbL) thin films, which comprise a PANi/SWNT-PEDOT:PSS repeating sequence, made by the spraying method is greater than that of the same ones assembled by traditional dip coating. The surface structure of multilayer thin films constructed by the spraying approach show excellent coverage of highly networked individual and bundled SWNT, which is similarly to what is observed when carbon nanotubes-based LbL assemblies are formed by classic dipping. The multilayer thin films via the spray-assisted LbL process exhibit significantly improved TE performances. A 20-bilayer PANi/SWNT-PEDOT:PSS thin film (~90 nm thick) yields an electrical conductivity of 14.3 S/cm and Seebeck coefficient of 76 μV/K. These two values translate to a power factor of 8.2 μW/m·K2, which is 9 times as large as the same films fabricated by a classic immersion process. We believe that this LbL spraying method will open up many opportunities in developing multifunctional thin films for large-scaled industrial use due to rapid processing and the ease with which it is applied.