A pen with adjustable holding structure is essentially for the user to write with his/her specified finger to lean against a stop protuberance. The pen has a penholder with a writing end formed at its front tip for writing. The stop protuberance is provided ahead of the holding position, and an adjustable holding part is formed on the penholder behind the stop protuberance. With this structure, when manipulating the pen, the user may select one of five fingers as a specified one to lean against the stop protuberance to settle thereat. The adjustable holding part is bendable at random according to the user's manipulation habit so as to lead the specified finger to lean against the best position on the stop protuberance to perform writing with the pen.