Qubes OS is a security-oriented operating system (OS). The OS is the software that runs all the other programs on a computer. Some examples of popular OSes are Microsoft Windows, Mac OS X, Android, and iOS. Qubes is free and open-source software (FOSS). This means that everyone is free to use, copy, and change the software in any way. It also means that the source code is openly available so others can contribute to and audit it.
Not all virtual machine software is equal when it comes to security. You may have used or heard of VMs in relation to software like VirtualBox or VMware Workstation. These are known as “Type 2” or “hosted” hypervisors. (The hypervisor is the software, firmware, or hardware that creates and runs virtual machines.) These programs are popular because they’re designed primarily to be easy to use and run under popular OSes like Windows (which is called the host OS, since it “hosts” the VMs). However, the fact that Type 2 hypervisors run under the host OS means that they’re really only as secure as the host OS itself. If the host OS is ever compromised, then any VMs it hosts are also effectively compromised.
By contrast, Qubes uses a “Type 1” or “bare metal” hypervisor called Xen. Instead of running inside an OS, Type 1 hypervisors run directly on the “bare metal” of the hardware. This means that an attacker must be capable of subverting the hypervisor itself in order to compromise the entire system, which is vastly more difficult.
Qubes makes it so that multiple VMs running under a Type 1 hypervisor can be securely used as an integrated OS. For example, it puts all of your application windows on the same desktop with special colored borders indicating the trust levels of their respective VMs. It also allows for things like secure copy/paste operations between VMs, securely copying and transferring files between VMs, and secure networking between VMs and the Internet.