Using Zoom Filters:
It may sound weird but zoom filter can help to reduce brightness below minimum level. Here is how you can do this.
Go to Settings>General>Accessibility>Zoom Switch on Zoom function. Now when you will double tap with three fingers the screen will be zoomed in. Now go do zooming options by tapping on the rectangular box given at the bottom of zoom frame From zooming options set zoom level to minimum and then tap on Zoom Filters and choose Low light. You will find that zoomed window is dimmed below the minimum brightness level. Now in custom region Choose full screen and now the brightness for your whole screen will be below the minimum level of brightness. Tap home button and use your device with low brightness and if you want to restore to normal brightness just double tap with three fingers on the screen or turn off zoom in Settings>General>Accessibility>Zoom.
This is how zoom filters can help you to reduce brightness of your iPhone screen below minimum level.
By Reducing White Point:
Another method to reduce brightness below minimum level is reducing white point. Because the base of every bright color is white so reducing white point is a good idea to lower down brightness. This is how you can do this on your iPhone.
Go to Settings>Accessibility>Display accommodations. Turn on the switch given next to Reduce white point. You will see a slider below Reduce white point button set it to 100% and you will find that brightness is reduced.
This is how you can choose to reduce brightness of your iPhone by using these two methods. Now using your iPhone in dark will not strain your eyes.