The single-phase nanoscale Sr$_{2}$FeMoO$_{6-\delta}$ powders with various degrees $P$ of superstructural ordering of Fe$^{3+}$ and Mo$^{5+}$ cations are obtained with the use of citrate-gel method at pH = 4, 6, 9 ($P$ = 65% for pH = 4, $P$ = 51% for pH = 6, and $P$ = 20% for pH = 9). The sequence of phase transformations is studied, the temperature ranges of formation and dissolution of associated phases of SrMoO$_{4}$, SrCO$_{3}$ and Fe$_{3}$O$_{4}$ are determined by the methods of X-ray diffraction, thermogravimetric analysis, atomic force microscopy (AFM) and scanning electron microscopy (SEM), and dynamic light scattering (DLS analysis). Due to studying the sequences of phase transitions during crystallization of strontium ferromolibdat by the citrate-gel method with pH = 4 of the initial solution, the mixed regimes of synthesis of a single-phase Sr$_{2}$FeMoO$_{6-\delta}$ compound with an average grain size of 50–120 nm and with maximum ($P$ = 88%) degree of superstructural ordering of the Fe and Mo cations are developed. According to the method of X-ray photoelectron spectroscopy, in the obtained powders of Sr$_{2}$FeMoO$_{6-\delta}$, it is found a mixed valence state of the Fe and Mo cations, in which the Fe$^{2+}$ concentration increases with pH, and the concentration of Fe$^{3+}$ decreases. According to the temperature dependences of magnetization measured in ZFC and FC regimes, in powders of Sr$_{2}$FeMoO$_{6-\delta}$ ferrimagnetic, an unstable superparamagnetic state is determined at T < 19 K. As found, an external magnetic field exceeding the value of the magnetic anisotropy field stimulates the transition in nanosize grains from the metastable superparamagnetic state into a stable superparamagnetic state. Herewith, in the powders at pH = 4, the amount of nanoscale grains is greater than at pH = 6 and 9 that leads to their greater magnetization at T = 4.2–19 K.