With the wide application of nanomaterials in biomedical detection in recent years, hybridization methods which use nanoparticles as solid phase hybridization carriers have emerged. However, commercial equipments, such as conventional thermal cyclers and hybridization ovens are usually not appropriate for DNA hybridization on the surface of nanoparticles. We designed and improved a total temperature micro-volume blended incubating and hybridizing apparatus (TTMHA), which can be used for blending and suspending of nanoparticles in a small volume and liquid phase environment. This device highlights the mechanical rotation structure which can not only provide a uniform temperature field, but also makes the liquid flow fully in the reaction system and improves DNA hybridization efficiency significantly. A complex PID control algorithm, including Bang-Bang control and Fuzzy-PID control algorithm, was applied in this research project to improve the control accuracy and stability. Furthermore, a model detection experiment using ssDNA (single strand DNA) sequence was conducted in thermal cyclers and TTMHA respectively to verify the optimal hybridization efficiency of the TTMHA.