We systematically investigated the effect of 2,5-bis(2-hydroxy-3-methacryloyloxypropoxy)-1,4:3,6-dianhydro-sorbitol (Iso-GMA) with different concentrations on the structural and morphological evolution of poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) containing a fixed volume of dimethyl sulfoxide (DMSO) to realize water-resistant organic thermoelectric devices. As an additive, Iso-GMA is a hydrophilic and crosslinking agent that can interact with PEDOT and PSS chains by hydrogen bonding and/or dipole-dipole- or dipole-charge-interaction. The Seebeck coefficient and power factor in the film incorporating 3.0 vol% DMSO and 0.8 vol% Iso-GMA were respectively 1.82 × 102 and 1.53 × 105% higher than those of the pristine PEDOT:PSS film without additives (DMSO and Iso-GMA). These results can be attributed to the self-assembled and crosslinked fibril networks with optimized phase separation, where the film has densely-packed PEDOT and highly lamellar-stacked PSS. Also, the reduced charge carrier concentration from the structural characteristics originated in the higher thermoelectric properties. We introduced the schematic illustration to understand the chemical bonding among the components and the morphological evolution according to the Iso-GMA concentration. The increased mechanical strength by the interchain stacking degree of PEDOT and the crosslinking of Iso-GMA facilitate the film remained in a water bath for 0.5 h without physical degradation, and sustain the thermoelectric properties during 12 h in humid conditons.