Gene detecting methods without using PCR are disclosed. The methods comprise forming sandwich complexes by target genes with nano-probes and capture probes, wherein nano-probes are modified with recognition molecules and magnetic microparticles modified with capture molecules; then separating the sandwich complexes; releasing the nano-probes; and detecting molecular ion peaks of encoding molecules on the surface of nano-probes by mass spectrometric detection directly, characterized in that the proportions of recognition molecules and encoding molecules on the nano-probes are 300-2000:1.