It’s an excellent question.
And the answer is…
… we don’t know.
Hypnosis is complex. It’s kind of like asking ‘what happens in the brain during thinking?’ There probably is an answer to that question, but we certainly don’t know it yet.
Having said that, there is a lot we do know. Aside from all our unanswered questions, we have the results of research, measurement and experimentation. These all provide clues as to what happens, physically, during hypnosis.
Physical Effect 1: Blood Flow
One thing we can say, without doubt, is that there is a physical change. Hypnosis isn’t something that people imagine or fake. There are definite, measurable differences when a person is hypnotised. And a key one is blood flow. Hypnosis changes the way blood flows to certain brain regions, especially those responsible for sensing pain and cognition.
What’s harder to say is whether hypnosis increases or decreases blood flow to these regions. It could be ‘both’? Or ‘it depends’? Something seems to happen.
Physical Effect 2: Brain Waves
Now, here’s an interesting one. And it’s not at all surprising, given what hypnosis can do.
Brain cells communicate using electrical impulses. Charged particles and other properties of the cells create these impulses. This creates brain waves – signals of electrical activity that we can measure.
Different frequencies of brain waves are associated with different mental states. And what researchers found is that hypnosis induces specific frequencies that relaxation alone can’t.
Again, we have a unique response from the brain – something measureable – in response to hypnosis.
Physical Effect 3: Internodal Activity
There are different nodes in the brain, specialised for different tasks. In general, there is some connectivity and some isolation between these structures in the brain. Hypnosis influences this connectivity.
Like with blood flow, hypnosis seems to both increase and decrease connectivity. It has the most dramatic results on left-right hemisphere connectivity, as well as a few functions of interest:
“[Hypnosis leads to] perhaps higher levels of structural connectivity between left and right hemisphere frontal areas and between frontal areas and the ACC.”
The frontal areas control our focus, reasoning and willpower. The ACC, or anterior cingulate cortex, governs things like reward, motivation and determination. This could explain how hypnosis can improve your motivation to overcome challenges.
Your Brain on Hypnosis
The brain is the most complicated thing in the known universe. As such, we don’t have all the answers. No doubt, this is only a glimpse of what happens during hypnosis. But the key thing to remember is that real, physical changes do occur. Hypnotism changes the way the brain works. It modifies it and strengthens it. And these improvements lead to improvements in your life.
 Effects of hypnosis on regional cerebral blood flow during ischemic pain with and without suggested hypnotic analgesia.; Crawford HJ1, Gur RC, Skolnick B, Gur RE, Benson DM.; Int J Psychophysiol. 1993 Nov;15(3):181-95.  The origin of extracellular fields and currents--EEG, ECoG, LFP and spikes.; Buzsáki G1, Anastassiou CA, Koch C.; Nat Rev Neurosci. 2012 May 18;13(6):407-20.  Differentiation of hypnosis and relaxation by analysis of narrow band theta and alpha frequencies.; Williams JD1, Gruzelier JH.; Int J Clin Exp Hypn. 2001 Jul;49(3):185-206.  MECHANISMS OF HYPNOSIS: Toward the Development of a Biopsychosocial Model; Mark P. Jensen, Tomonori Adachi, Catarina Tomé-Pires, Jikwan Lee, Zubaidah Jamil Osman, and Jordi Miró; Int J Clin Exp Hypn. 2015; 63(1): 34–75.  A Multifaceted Hypnosis Smoking-Cessation Program: Enhancing Motivation and Goal Attainment; Joseph P. Green & Steven Jay Lynn; International Journal of Clinical and Experimental Hypnosis, Volume 65, 2017 - Issue 3