The Inner Sanctum has received generally positive reviews from critics. Eduardo Rivadavia of Allmusic gave the album three and a half out of five stars, and commented that Saxon continued "to do their legacy proud as they move through their third decade of recording activity." He described the album's first three tracks as "frantic" and the third, "Let Me Feel Your Power" as "jaw-dropping", and also praised the "majestic" "Red Star Falling", comparing it to the band's earlier songs "Dallas 1PM" and "Broken Heroes", although he was critical towards the single version of "If I Was You", advising the listener to "make sure your CD contains the album version". Rivadavia concluded his review by saying "although it's certainly not perfect by any stretch, The Inner Sanctum is welcome addition to this band's sizeable discography, and, pound for pound, might just take the crown as Saxon's best album of the early 2000s." The album was also awarded an 8/10 in the UK's Metal Hammer magazine.
However, Andy Lye of Jukebox:Metal was more critical in his review of the album, giving it three out of five stars, and criticising its opening track "State of Grace", calling it "derivative and largely boring", and also "Let Me Feel Your Power" commenting that "a great, grooving mid-section can't quite save it from its appalling lyrics and tired riffs." He went on to call "I've Got to Rock (To Stay Alive)" "as bad as you'd expect" and criticised "If I Was You" for sounding "exactly like all metal singles sound". He concluded by stating that "Against the wider metal market this is an average album (hence three stars), but against recent Saxon output it is comfortably below average."