FlexSim includes a standard object library, with each object containing pre-built logic and task execution to mimic the resources found in real-world operations. FlexSim objects are defined and programmed in four classes: fixed resource class, task executer class, node class and visual object class. FlexSim uses an object-oriented design.

The logic for a FlexSim model can be built using very little or no computer code. Most standard objects contain an array of drop-down lists, properties windows, and triggers that allow the user to customize the logic required for an accurate model of the system. FlexSim also includes a flowcharting tool to create the logic for a model using pre-built activity blocks.

Users can build the model by dragging and dropping predefined 3D objects into a "model view" to layout and link the model. Experienced users also have the option to specify and modify object parameters and behaviors using FlexScript and C++ programming languages.