The invention discloses intrinsic hydrophobic polyimide aerogel and a preparation method as well as an application thereof. The structure of the aerogel is shown in a structural formula (I); special groups, such as a hydrophobic fluorin-containing group and an alicyclic group at low polarity are introduced to a polyimide molecular structure to endow a polyimide aerogel material with excellent hydrophobic performance; in addition, the polyimide aerogel has the characteristics of high porosity, low heat conductivity, low density, large specific surface area, low dielectric constant, low dielectric loss and the like, and therefore is of significant application values in the fields of thermal insulating components of spacecrafts, such as airplanes and satellites, interlayer dielectric materials of super-large-scale integrated circuits, thermal insulating layers of buildings, environment protection, deep ocean detection, oil exploration, energy-saving buildings, household appliances, warm-keeping clothes, sports equipment and the like. Formula I is shown in the specification.