In the JSAPI, JSRuntime is the top-level object that represents an instance of the JavaScript engine. A program typically has only one JSRuntime, even if it has many threads. The JSRuntime is the universe in which JavaScript objects live; they can't travel to other JSRuntimes.
All JavaScript code and most JSAPI calls run within a JSContext. The JSContext is a child of the JSRuntime. A context can run scripts. It contains the global object and the execution stack. Exception handling, error reporting, and some language options are per-JSContext. Once created, a context can be used any number of times for different scripts or JSAPI queries. For example, a browser might create a separate context for each HTML page; every script in the page could use the same context.
Objects may be shared among JSContexts within a JSRuntime. There's no fixed association between an object and the context in which it is created.
Sample code to set up and tear down a JSRuntime and a JSContext is at JSAPI User Guide.
Threads
Only one thread may use a JSContext or JSRuntime. Earlier versions allowed using JS_ClearContextThread and other functions to move a JSContext from one thread to another. This feature has since been removed.