||In this study, we presented a spatially-controlled molecular patterning technique to prepare liquid crystal (LC) microdroplet arrays on glass substrates. This technique utilizes an oxygen plasma activated PDMS stamp to remove the pre-coated dimethyloctadecyl 3-(trimethoxysilyl) propyl ammonium chloride (DMOAP) molecules from glass substrates, producing a surface with complementary patterns and specific hydrophobicity. When LC molecules are introduced onto this produced molecular pattern, a LC microdroplet array with uniform droplet size and positional order is formed. By using the LC microdroplet array doped with a Hg2+ selective ligand, the lowest detectable concentration of Hg2+ is 200-fold lower than that of conventional LC-based sensors. In addition, multiplexed detection of Hg2+, Al3+, Fe3+ and pH value in real water samples with a high recovery rate (∼100%) was demonstrated by using the LC microdroplet arrays doped with different molecular probes. Due to the specific arrangement of the LC microdroplet arrays, the collected optical signal of LC microarrays can be transformed into numerical symbols. The developed spatially controlled molecular patterning technique could be used to prepare highly uniform LC microdroplet arrays with consistent optical signals, providing a simple method to prepare the LC-based sensing platforms with improved sensing performance.