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We present a novel alternating joint inversion algorithm for controlled-source electromagnetic (CSEM) and seismic data. The two different physical parameters, i.e., the electromagnetic (EM) resistivity and seismic velocity, are correlated using the structural constraint during the inversion. The structural coupling used is the joint total variation (JTV) constraint, which is incorporated into the objective function of the individual EM or seismic inversion to enforce the structural similarity between the resistivity and velocity. The conventional cross-gradient constraint is not preferred as it can only be used for enforcing structural similarity for 2-D or 3-D case since it is always zero for 1-D joint inversion. The JTV constraint can be applied for 1-D joint inversion, as well as for the 2-D/3-D case, which is of a broader interest. The improved Gauss–Newton (GN) is used for minimizing the objective function and for reconstructing the subsurface resistivity and velocity. The alternating joint inversion algorithm is applied for integrating the CSEM data with cross-well seismic data for subsurface reservoir evaluation and water–oil identification. Numerical examples show that the developed joint inversion can improve the inversion results significantly over those from the separate EM or seismic inversion.