Removing ultraviolet noise from the gauge fields is necessary for glueball spectroscopy in lattice QCD. It is known that the Yang-Mills gradient flow method is an alternative approach instead of link smearing or link fuzzing in various aspects. In this work we study the application of the gradient flow technique to the construction of the extended glueball operators. We examine a simple application of the gradient flow method, which has some problems in glueball mass calculations at large flow time because of its nature of diffusion in space-time. To avoid this problem, the spatial links are evolved by the “spatial gradient flow”, that is defined to restrict the diffusion to spatial directions only. We test the spatial gradient flow in calculations of glueball two-point functions as a new smearing method, and then discuss its efficiency in comparison with the original gradient flow method and traditional smearing methods.