What may be understood from your question is that this work for which you receive this percentage as commission is separate from your regular work with the company, for which you receive a fixed salary every month.
So this work is under a separate contract between you and the company, and your payment for it is this commission. The scholars differed as to whether it is permissible to make the payment a percentage of the profits.
Imam Ahmad (may Allah have mercy on him) was of the view that that is permissible.
This has been discussed previously in the answer to question no. 134658.
Based on that, there is nothing wrong with you taking this commission in payment for the work that you do.
And Allah knows best.