The invention relates to a method and device for jointly detecting SNV, CNV and FUSEON variations. More specifically, the device comprises a sequencing data reading module, an SNV detection module, a CNV detection module, a FUSEON variation detection module and a result output module, wherein the CNV detection module comprises a BAF calculation module, a BAF correction module, a BAF separation and identification module, a sequencing depth calculation module, a logR correction module, a logR background noise calculation module and a CNV judgment module. The method and device, based on BAF+logR information, detect the SNV, CNV and FUSEON variations in a sample with an extremely low ctDNA proportion, especially the CNV variation with low copy number amplification, with high sensitivity and high specificity.