During the kedusha at mincha and shacharis prayer service, the custom is to bob up and down when saying kadosh, kadosh, kadosh.
what is the reason for this?
You are duplicating the action of the ministering angels which are mentioned in the opening blessings before the recital of Shema. It says "The Ofanim and the Holy Chayot, with a great commotion, ascend to the place of the Seraphim..."
The concept is explained in the "כגונא דאנון מתיחדין לעלא באחד" prayer that is said in Kabbalat Shabbat before Barchu. The Angels above do the same Avodah which we do below. Through this parallel behavior we fulfill the posuk, "HaShem is one and his name (שמו) is one." The word 'name', (שם) is also an abbreviation for ׳שמים ומלכות׳, An allusion to the Heavens above, meaning the Angels and the level of Malchut, a reference to here below in the material, physical realm. G-d's kingship and unity is manifest above and below.
Nefesh HaChaim explains that it is to demonstrate that through our Kedusha we are elevating the spiritual spheres of existence.
R' Yonasan Eibshutz says we are mimicking the angels, who go up and down, as Yechezkel 1:14 describes their motion as רצוא ושוב - if they get to a point "too close" to Hashem, they will become intimately aware of their lack of existence (and the existence of anything other than Hashem) and will cease to be. So they go up and then come back down. We do the same, as we must balance between the recognition of the reality that ein od milvado - there is nothing other than Hashem - while still living with the sense of our autonomy.
Reishis Chochma explains that we raise ourselves up to show that we want to be kadosh also.
[This is all from my early notes when I was less scrupulous about detailed sourcing. I'll have to look to find exact citations]