If you want Slic3r to generate Gcode with a temperature change at a specific height (e.g. for printing a temperature tower), you will need to add a line of conditional G-code.
To do that, click on the Printer Settings tab and in the left sidebar on Custom G-code.
In the text field After layer change G-code add a line like the following for each desired temperature change:
{if layer_z==10}M104 S190{endif}
This example changes the extruder temperature at a height of 10mm to 190°C.