Abstract Phase engineering is an important strategy to modulate the electronic structure of molybdenum disulfide (MoS2). MoS2-based composites are usually used for the electromagnetic wave (EMW) absorber, but the effect of different phases on the EMW absorbing performance, such as 1T and 2H phase, is still not studied. In this work, micro-1T/2H MoS2 is achieved via a facile one-step hydrothermal route, in which the 1T phase is induced by the intercalation of guest molecules and ions. The EMW absorption mechanism of single MoS2 is revealed by presenting a comparative study between 1T/2H MoS2 and 2H MoS2. As a result, 1T/2H MoS2 with the matrix loading of 15% exhibits excellent microwave absorption property than 2H MoS2. Furthermore, taking the advantage of 1T/2H MoS2, a flexible EMW absorbers that ultrathin 1T/2H MoS2 grown on the carbon fiber also performs outstanding performance only with the matrix loading of 5%. This work offers necessary reference to improve microwave absorption performance by phase engineering and design a new type of flexible electromagnetic wave absorption material to apply for the portable microwave absorption electronic devices.