The reality TV star, 29, who recently joined the cast of 'Keeping Up with the Kardashians' to try to repair his strained relationship with Bruce, 63, reportedly blames his stepmother Kris Jenner for their issues.
A source told gossip website RadarOnline.com: ''Brody has had a lifetime of this and he holds Kris responsible for Bruce not being a bigger part of his life when he was a child.
''Kris wouldn't let Bruce spend time with Brody and (his older brother) Brandon when they were young because it would be time kept away from her, and when Kris became pregnant with Kendall and Kylie, the boys hardly ever saw their father. Kris is very persistent and used to getting what she wants, and Brody and Brandon suffered because of it.''
The insider added: ''(Brody) wishes his dad would just divorce Kris. Bruce and Kris are leading separate lives and don't even share a bedroom together anymore. He has been spending a lot of time at his Malibu rental without Kris. Brody wants to be closer to his dad, but it's very hard with Kris in the picture, because she always has to make everything about her.''
It was previously reported that Bruce was ''really upset'' about how his relationship with his older sons, Brandon, 32, and Brody, who were primarily raised by their mother Linda Thompson and ex-stepfather David Foster, was being portrayed on the family's E! reality series.
A source recently said: ''He thought this season was going to show the two families coming together and not all of this negativity about events that happened decades ago.
''Kris is an executive producer on the show and has the final approval about what viewers see. Bruce is ticked off his relationships with his sons is being used to make him look bad. He's livid. He is an amazing father to Kendall and Kylie and is around for them much more than Kris.''
Bruce has six biological children of his own, as well his four famous stepchildren, Kourtney, Kim, Khloe and Rob Kardashian.