The green alga Chromochloris zofingiensis is able to accumulate value-added ketocarotenoids and represents an alternative producer with industrial production potential. To further understand the biosynthesis of ketocarotenoids, we generated mutants of C. zofingiensis and obtained two (czchy1 and czchy2) with profound changes in carotenoid profile. Both mutants showed a considerably higher level of canthaxanthin than the wild type (WT), with czchy1 being more significant. Clearly, among various stress conditions, czchy1 accumulated the highest level of canthaxanthin under the combination of high light and nitrogen deprivation (HL + ND), which was more than doubled of WT. Prolonged induction of HL + ND allowed canthaxanthin of the alga to reach 2.8 mg g−1 of dry weight, which could be further promoted by the addition of fulvic acid. czchy1 also had higher β-carotene level and lower levels of astaxanthin, lutein and zeaxanthin than WT. Molecular characterization of czchy1 revealed that the β-carotene hydroxylase (CHYb) gene possessed a point mutation and encoded an enzyme with attenuated hydroxylating activity. Besides, in czchy1 as compared to WT, CHYb was transcriptionally down-regulated, β-carotene hydroxylase (BKT1) and lycopene β-cyclase (LCYb) were transcriptionally up-regulated. Therefore, czchy1 likely adopted a multiple strategy combining pull, push and impairment of competing pathway towards boosting canthaxanthin accumulation.