During the preparation of soft-nanocomposites, ultrasonic treatment is widely utilized to improve the dispersion of nanomaterial in the gel system. However, both the nanomaterials and the low molecular weight organic gelators (LMWGs) could interact with the ultrasonic energy. In this paper, the influence of ultrasonication in the microstructure and properties of 12-hydroxystearic acid (12-HSA) soft-nanocomposites with LaF3 nanoparticles were investigated. It was found that despite ultrasonication could improve the dispersion of LaF3 nanoparticles, the viscoelastic properties of the gel system were greatly changed. Via characterizing the xerogel, the ultrasonic-induced fining effect in gelator fibers was confirmed, which accounted for the changed gel properties. Tribological evaluations show that the 12-HSA gel with coarse fibers shows better performance under low load, while the one with fine fibers exhibits better performance under higher load. With the aid of LaF3 nanoparticles, the adaptability of soft-nanocomposites for severe conditions could be further improved due to the cooperative effects between 12-HSA and LaF3 nanoparticles in constructing the boundary lubricating films. Although the nanomaterials are effective to improve the functionality of LMWG gels, the microstructure of gelator assembly and gel properties could be also significantly changed during the dispersion process of nanomaterials via sonication.