A simultaneous wide-angle and small-angle X-ray scattering study of two poly(ethylene naphthalene 2,6-dicarboxylate) samples crystallized from the glassy state at different annealing temperatures for different annealing times was carried out with synchrotron radiation. Either single or dual melting was induced in the samples, as confirmed by differential scanning calorimetry (DSC). The correlation function and interface distribution function were calculated to evaluate microstructural parameters such as the long spacing, the thickness of the amorphous and crystalline phases, and the width of the size distributions. The sample with dual melting behavior exhibited an abrupt increase of all microstructural parameters at temperatures above the melting of the lowest endotherm, whereas the sample revealing a single melting endotherm did not show such a sudden change. This finding agrees with the concept that the appearance of two melting peaks in DSC traces can be explained by the dual lamellar stacking model.