Although gold nanoparticles (GNPs) are promising probes for biological imaging because of their attracting optical properties and bio-friendly nature, properties of the multi-photon (MP) emission from GNP aggregates produced by a short-wave infrared (SWIR) laser have not been examined. In this paper, characterization of MP emission from aggregated 50 nm GNPs excited by a femtosecond (fs) laser at 1560 nm is discussed with respect to aggregate structures. The key technique in this work is single particle spectroscopy. A pattern matching technique is applied to correlate MP emission and SEM images, which includes an optimization processes to maximize cross correlation coefficients between a binary microscope image and a binary SEM image with respect to xy displacement, image rotation angle, and image magnification. Once optimization is completed, emission spots are matched to the SEM image, which clarifies GNP ordering and emission properties of each aggregate. Correlation results showed that GNP aggregates have stronger MP emission than single GNPs. By combining the pattern matching technique with spectroscopy, MP emission spectrum is characterized for each GNP aggregate. A broad spectrum in the visible region and near infrared (NIR) region is obtained from GNP dimers, unlike previously reported surface plasmon enhanced emission spectrum.