[6] The album consists of five tracks with song durations ranging from 7 to 17 minutes that deal with events and people important in Newsom's life, including the sudden death of her best friend, a continuing illness and a tumultuous relationship.

[19] Describing it as "incredibly likeable, and more convivial than the twee Milk Eyed Mender", Jimmy Newlin of Slant Magazine dubbed Ys "a precious—in every sense of the word—masterpiece".

[22] Uncut's John Mulvey felt that though its "vast scale" opens up the potential for "self-indulgence" and "prog folly", upon listening to the record "all the doubts evaporate.

"[3] Heather Phares of AllMusic described Ys as "a demanding listen, but it's also a rewarding and inspiring one",[13] while Alexis Petridis of The Guardian concluded that the album is a "hard sell, perhaps, but it could be the best musical investment you make all year".

[15] Pat Long of NME wrote that Newsom "has managed to lessen the twee factor of her last record, in the process crafting an album as bewitching as it is odd".

[18] Leah Greenblatt of Entertainment Weekly felt that Newsom "remains an acquired taste", but that Van Dyke Parks' contributions and the album's orchestration "have an ameliorating effect on the too-precious warble that either bewitches or repels.

"[14] The Independent's Andy Gill wrote that Ys "leaves one in no doubt of her oddball credentials" and "rarely, if ever, has an artist so assiduously cultivated cult status".

[16] Among negative assessments, Rolling Stone critic Christian Hoard called the album "hard to stomach" and plagued by overlong tracks "with meandering strings-and-things accompaniment and indulgent vocal quirks that make Björk sound like Kelly Clarkson.

"[20] Robert Christgau, in his Consumer Guide column for MSN Music, wrote that much of the "sprightly" qualities of The Milk-Eyed Mender had been "subsumed here by ambition, to be kind, and privilege, to be brutally accurate", and that the songs "reveal only that her taste for the antique is out of control".

Dubbing it Newsom's "greatest achievement", Drowned in Sound's Adam Turner-Heffer credited her and the album with proclaiming US indie music as "the dominant force" for the remainder of the 2000s.

[29] Strand of Oaks' Timothy Showalter expressed his admiration of the album and Newsom's lyrical gifts, writing that she "stands at some grander place than me, and I am deeply reassured by that".

Gigwise named Ys the 32nd greatest album of the 2000s commenting that "the record rightly received blanket acclaim upon its initial release and is already sounding better with age.

[46] In 2020, Daniel Radcliffe selected the song "Emily" as one of his choices for the BBC Radio 4 program Desert Island Discs, describing Newsom as an artist "who gets weirder and more wonderful and more imaginative every time she comes back".