In this paper, we focus on the super Kupershmidt operators (also called super -operators or relative Rota-Baxter operators) of a Malcev superalgebra. We first consider the relationship between Nijenhuis operators and super Kupershimidt operators. Then we discuss Kupershmidt-(dual-)Nijenhuis structures on a Malcev superalgebra. Moreover, we study the deformations of Nijenhuis elements and obtain a deformation theory of super Kupershmidt operators on a Malcev superalgebra. Communicated by Alberto Elduque