Time-of-flight secondary ion mass spectrometry (ToF-SIMS) is a surface analytical technique for compositional information at the surface of a specimen with high sensitivity. With the continuing development of new primary ion sources such as liquid metal ion guns or gas cluster ion beams, ToF-SIMS has been a promising tool for analyzing small molecules like metabolites and lipids in biological samples. However, accelerated ions used in ToF-SIMS analysis require an ultra-high vacuum environment, which limits its application to solid or dried specimens, and matrix effects hinder quantitative analysis. Here we propose a novel method for quantitative ToF-SIMS analysis of amino acids in a solution by freeze-drying them into a homogeneously mixed matrix substrate. We fabricated a parylene-based microarray platform consisting of a thin parylene film patterned into an array of wells of 1 mm diameter on a silicon substrate. Sub-microliter drops of solution samples, prepared by adding an analyte, standard material, and high concentration matrix to distilled water, can be manually loaded on the exact spot of each well surrounded by a hydrophobic parylene barrier with ease. Every solution drop is frozen and then dried at a low temperature, turning into a flat continuous phase matrix still homogeneously mixed with the analyte and standard material. We show that ToF-SIMS can quantitatively analyze amino acids at micromolar concentrations using stable isotope-labeled phenylalanine as a matrix substrate and a stable isotope-labeled valine as a standard for normalization.