Scalar fields play an important role in constructing modified gravity theories. In the case of a single scalar field with timelike gradient, the corresponding Lagrangian in the unitary gauge takes the form of spatially covariant gravity (SCG), which is proved useful in analyzing and extending the generally covariant theories. In this work, we apply the SCG method to the scalar-nonmetricity theory, of which the Lagrangian is built of the nonmetricity tensor and a scalar field. We derive the 3+1 decomposition of the geometric quantities and especially covariant derivatives of the scalar field up to the third order in the presence of a nonvanishing nonmetricity tensor. By fixing the unitary gauge, the resulting Lagrangian takes the form of a SCG with nonmetricity, in which all the ingredients are spatial tensors. We then exhaust the scalar monomials of SCG with nonmetricity up to d=3\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d=3$$\\end{document} with d the total number of derivatives. Since the disformation tensor plays as an auxiliary variable, we take the Lagrangian with d=2\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$d=2$$\\end{document} as an example to show that after solving the disformation tensor, we can get an effective SCG theory for the metric variables but with modified coefficients. Our results provides a novel approach to extending the scalar-nonmetricity theory.