Flexure nanopositioner is usually utilized to compensate the alignment deviation in the process of micro/mini LED chip repairing.However, thermal distortion effect always reduces the alignment accuracy of the precision positioning system, which will seriously affect the chip repairing quality. The motivation of this article is to develop a novel decoupled flexure nanopositioner with thermal distortion self-elimination function. The thermal distortion self-elimination performance is achieved via three flexible connection modules (FCM), in which the thermal stress can be automatically eliminated. First the design, modeling, and optimization of the proposed flexure nanopositioner are presented. Then, theoretical analysis in terms of thermal deformation relationship derivation and whole mechanism compliance modeling are carried out, respectively. In addition, aiming for minimizing thermal distortion of the nanopositioner, the FCM is optimized by the genetic optimization algorithm and finite element analysis (FEA) evaluations. Finally, a series of validation experiments including displacement decoupling, tracking performance at different temperatures, and thermal distortion elimination tests are successfully carried out. The theoretic, simulated, and practical testing results uniformly indicate that thermal distortion can be eliminated up to 61.6% by FCM, the displacement coupling error is kept within 2.4%, and the closed-loop positioning precision is <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\pm$</tex-math></inline-formula> 100 nm with 48- <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$\mu$</tex-math></inline-formula> m stroke. All the experimental results verify that the developed flexure nanopositioner can achieve decoupling, accurate, and stable positioning targeted the ultra-precision positioning tasks under the condition of environmental temperature drift.