How to increase executionTimeout for a long-running query?

Execution Timeout is 90 seconds for .NET Framework 1.0 and 1.1, 110 seconds otherwise.

If you need to change defult settings you need to do it in your web.config under <httpRuntime>

<httpRuntime executionTimeout = "number(in seconds)"/>

But Remember:

This time-out applies only if the debug attribute in the compilation element is False.

Have look at in detail about compilation Element

Have look at this document about httpRuntime Element