This paper reports on the comparative investigation of nanocrystal structure and luminescence properties of Er3+/Yb3+-codoped gadolinium molybdate nanocrystals Gd2(MoO4)3 and Gd2MoO6 synthesized by the Pechini method with citric acid and ethylene glycol. Their crystallization, structure transformation, and morphologies have been investigated by X-ray diffraction, thermogravimetric/differential scanning calorimetry, and transmission electron microscopy. It is noticed that Er3+/Yb3+-codoped monoclinic Gd2(MoO4)3 nanocrystals have shown an intense upconversion through a sintering of the organic complex precursor at 600°C. Furthermore, it transforms to orthorhombic Gd2(MoO4)3 when the precursor is sintered at 900°C. In counterpart of monoclinic Gd2MoO6, however, the monoclinic structure remains unchanged when the precursor is sintered at a temperature ranging from 600°C to 900°C. Intense visible emissions of Er3+ attributed to the transitions of 2H11/2, 4S3/2–4I15/2 at 520 and 550 nm, and 4F9/2–4I15/2 at 650 nm have been observed upon an excitation with a UV source and a 980 nm laser diode, and the involved mechanisms have been explained. It is quite interesting to observe obvious differences both in the excitation and the upconversion emission spectra of Er3+/Yb3+-codoped Gd2(MoO4)3 respectively with monoclinic and orthorhombic structure. The quadratic dependence of fluorescence on excitation laser power has confirmed that two-photons contribute to upconversion of the green–red emissions.