Single-cell whole genome amplification (WGA) is a new technology, which can amplify small amounts of DNA from single cell and obtain the high coverage whole genome DNA template for revealing cell heterogeneity. Single cell WGA methods mainly include primer extension preamplification PCR (PEP-PCR), degenerate oligonucleotide primed PCR (DOP-PCR), multiple displacement amplification (MDA), and multiple annealing and looping-based amplification cycles (MALBAC). In this review, we describe the principles and applications of different single cell genome wide amplification, and we evaluate and compare their amplification efficiency, including the coverage of genome, homogeneity, reproducibility, and detection power of single-nucleotide variants (SNV) and copy number variants (CNV). The results show that MALBAC have the highest amplification homogeneity, the lowest allelic gene knockdown rate, the best reproducibility, and the best detection effect on CNV and SNV. We also describe the applications of MALBAC in human single sperm meiosis, aneuploidy analysis, and human oocyte genome research.