This work describes a program for computing and analyzing the ultrafast (attosecond and femtosecond) nonlinear X-ray spectra of molecules at the multiconfigurational quantum chemistry level, called MCNOX. It is aimed at cutting-edge current and future photochemistry/photophysics applications enabled by X-ray free-electron lasers and high harmonic generation light sources. It can compute steady-state X-ray absorption spectroscopy (XAS) and three types of ultrafast nonlinear X-ray spectra: transient XAS, all-X-ray four-wave mixing, and stimulated Raman spectra. It is especially capable of picking out major electronic transitions, and further computing the natural transition orbitals for these transitions, which help finally yield the physical and chemical insights from complex signals. Following a research paradigm of "electronic structure-*molecular dynamics-*signal", in this paper, methods for the former two steps are reviewed, and then the theory, implementations, and technical details for signal simulations are presented along illustrative examples on uracil.