Jason Koza said he did not allow his illustrations to be used in packaging for the album bought by Mr Shkreli.
The former drug executive - who owns the only copy of the album - has not issued any comment.
Mr Shkreli, 32, became infamous after his pharmaceutical firm hiked the price of an HIV drug by 5,000% last year.
Who is Martin Shkreli
Mr Koza, 34, said he thought his nine works would appear only on the website Wu Disciples.
In a legal complaint quoted by the Reuters news agency, Mr Koza said he was happy to have his work featured on the website, but had not given permission for it to be copied or displayed anywhere else.
He has blamed the band's leader Robert "RZA" Diggs for including them in the album, Once Upon a Time in Shaolin, bought by Mr Shkreli in an auction last year.
Mr Shkreli claimed at the time that he had no intention of listening to the album and had only bought it to "keep it from the people".
Mr Koza has also accused Mr Shkreli of allowing three works depicting three of the group's members to accompany a story on the Vice website.
The artist, a fan of the group, is seeking unspecified damages for copyright infringement.
Other defendants include Paddle8, which auctioned the album, and Wu Tang-affiliated producer Tarik "Cilvaringz" Azzougarh.
Wu Tang and Paddle8 have not commented on the case.
Last week, Mr Shkreli, former head of Turing Pharmaceuticals, refused to answer questions at a US congressional hearing on the company's pricing policy for the drug Daraprim, used by many AIDS patients.
Turing purchased the patent to the drug for $50m in July and, a month later, came to public attention for raising its price from 13.50 (£9.22) for a single dose to $750.
The Federal Trade Commission is also investigating whether Turing violated anti-trust laws when it raised the price of Daraprim.
In December, Mr Shkreli was arrested on securities fraud charges in a separate case. He denied the charges and was released on bail of $5m (£3.45m).
Martin Shkreli is facing a lawsuit claiming that his $2m (£1.38m) Wu-Tang Clan album includes work ripped off from a New York artist.