Complex genomes are noted to be extremely difficult to sequence or assemble by using ordinary methods. Complex genomes are typically characterized as being highly repetitive, highly heterozygous, extremely GC biased, or naturally contaminated, i.e., contaminations which cannot be removed before sequencing. To solve these problems with sequencing and assembling complex genomes, three major techniques include: (1) DNA extraction experiments, (2) Sequencing technologies and platforms, and (3) Algorithms and strategies for assembling. In this review, we summarize these state-of-the-art technologies and strategies used in these directions. We also review the representative projects of complex genome sequencing and address the development of these technologies and strategies for solving the challenges when sequencing or assembling complex genomes.