Why? For example if you run Fiji headless on a cluster and you would like it to use a fast local folder instead of a network drive.
This page tells you how you can pass on JVM arguments to Fiji upon start: http://fiji.sc/Java_Options
One can specify the “temp” directory using the following command:
$ fiji -Djava.io.tmpdir=~/tmp -- &
Double dash at the end is required to specify that the given argument is for Java.