XSPEC commands can be divided into 6 categories: Control, Data, Model, Fitting, Plotting and Setting, as follows:

- Control commands include items such as controlling logging, obtaining help, executing scripts, and other miscellaneous items to do with the program control rather than manipulating data or theoretical models.
- Data commands load spectral data and calibration data such as backgrounds and responses, and specify channel ranges to be fit.
- Model commands define and manipulate theoretical models and their parameters, and compute additional information such as fluxes or line identifications.
- Fit commands initiate the fitting routines, control the parameter set, perform statistical tests and compute confidence levels.
- Plot commands generate about 50 different kinds of 2-dimensional plots
- Setting commands change a variety of XSPEC internals which control details of models, statistics, and fitting methods.