Stranger Things 4 volume 2 has arrived which has given so many reveals regarding Vecna and the Upside Down. One of the burning questions was if Vecna created The Mind Flayer or was it the other way around.
Volume 2 has revealed that Vecna has been the show's villain all along. Vecna shows another flashback to Eleven, revealing that when he was banished to the Upside Down, he came to realize the Upside Down was a dimension untouched by human beings. At first, he became an explorer, wandering the Upside Down. Finally, he saw a mysterious cloud of particles, from which Vecna formed the Mind-Flayer.
These particles were the basis of the hive mind because anything that ingests them becomes caught up in it. In season 2, Will who was under influence of the hive mind - was freed from the Mind-Flayer's influence using extreme heat. That virus ultimately manifested as a stream of particles blasting out of Will's body into the night sky.
So Vecna created the Mind Flayer when he arrived in the Upside Down. Whenever Vecna kills someone, he acquires their consciousness and power. Connecting to the Mind Flayer's hive transformed Henry Creel into Vecna. Now he controls Demobats, Demodogs, and Demogorgons across the Upside Down.