The DNDC model is a process-base model of carbon (C) and nitrogen (N) biogeochemistry in agricultural ecosystems. This document describes how to use the PC Windows versions of the DNDC model for predicting crop yield, C sequestration, nitrate leaching loss, and emissions of C and N gases in agroecosystems. Part I provides a brief description of the model structure with relevant scientific basis. Part II describes how to install the model. Part III and IV demonstrate how to conduct simulations with the site and regional versions of DNDC, respectively. Part V provides basic information for uncertainty analysis with DNDC. Part VI contains six case studies demonstrating the input procedures for simulating crop yield, soil C dynamics, nitrate leaching loss, and trace gas emissions. A list of relevant publications is included in Part VII. These publications provide more information about the scientific background and applications of DNDC far beyond this User's Guide. DNDC9.3 can run in two modes: site or regional. By selecting the mode, the users will open a corresponding interface to manage their input information for the modeled site or region.