The invention discloses a primer, a probe composition and a kit for detecting a novel coronavirus and a variant thereof. The primer and the probe composition comprise specific primers and probes aiming at an ORF1ab gene, an N gene and a reference gene of SARS-CoV-2, and further comprises specific primers and probes aiming at one or more mutation sites of 69-70Del, L452R, E484K, E484Q and N501Y mutation sites of an S gene of the SARS-CoV-2, 106/107/108del mutation sites of an NSP6 gene, P71L mutation sites of an E gene, V82A mutation sites of an ORF7A gene and S253P mutation sites of an ORF3A gene. The primer, the probe composition and the kit disclosed by the invention can be used for detecting mutation sites while detecting the novel coronavirus, and can be used for distinguishing one or more of a B.1.351 variant, a B.1. 1.7 variant, a B.1.617 variant or a P.1 variant of the novel coronavirus; and the kit is a novel coronavirus and variant detection reagent which is rapid, low in cost and rich in variation information, and provides powerful help for global epidemic situation prevention and control and epidemic disease research.