This paper considers nonsquare spectral factors of nonlinear input a. ne state space control systems in continuous time. More specifically, we obtain a parametrization of nonsquare spectral factors in terms of a special class of inner-inner factorizations. Explicit formulas for different classes of spectral factors and related inner systems in terms of solutions of Hamilton-Jacobi equations are provided. Furthermore, the important notion of a minimal inner embedding for nonlinear control systems is introduced and used to derive several relationships between inner systems.