The current polymerase chain reactions‐based nucleic acid tests for large‐scale infectious disease diagnosis are always lab‐dependent and generate large amounts of highly infectious plastic waste. Direct non‐linear acoustic driven of microdroplets provide an ideal platform for contactless spatial and temporal manipulation of liquid samples. Here, a strategy to programmable‐manipulate microdroplets using potential pressure well for contactless trace detection is conceptualized and designed. On such contactless modulation platform, up to seventy‐two piezoelectric transducers are precisely self‐focusing single‐axis arranged and controlled, which can generate dynamic pressure nodes for effectively contact‐free manipulating microdroplets without vessel contamination. In addition, the patterned microdroplet array can act as contactless microreactor and allow multiple trace samples (1–5 µL) biochemical analysis, and the ultrasonic vortex can also accelerate non‐equilibrium chemical reactions such as recombinase polymerase amplification (RPA). The results of fluorescence detection indicated that such programmable modulated microdroplet achieved contactless trace nucleic acid detection with a sensitivity of 0.21 copy µL−1 in only 6–14 min, which is 30.3–43.3% shorter than the conventional RPA approach. Such a programmable containerless microdroplet platform can be used for toxic, hazardous, or infectious samples sensing, opening up new avenues for developing future fully automated detection systems.