Fluorescence lateral flow assays (FLFA) based on quantum dot probes have attracted significant attention in recent years due to their high sensitivity and quantitative detection capabilities. FLFA requires the use of a straightforward fluorescence reader for quantitative detection. Most fluorescence readers employ narrowband filters for auxiliary imaging, which facilitates the acquisition of high-contrast signals. However, during trace detection, the weak signal from FLFA can be easily lost due to optical flux loss associated with narrowband filters, thereby indirectly diminishing detection sensitivity. To address this issue, we developed a fluorescence signal reader that employs CMOS imaging without optical filters and proposed a highly sensitive signal detection algorithm based on continuous wavelet transform (CWT) to identify weak fluorescence signals with low contrast. Experimental results demonstrate that the method achieves a fluorescence detection sensitivity for quantum dots of 10⁻¹⁰ mol/L, with a relative standard deviation (RSD) of < 1.45%. The designed filter-free detection system and CWT analysis algorithm were applied to various FLFA systems (including the sandwich method and the competition method), with the correlation coefficient (R²) between all detection results and sample concentration exceeding 0.997. The findings of this study offer a highly sensitive signal detection method for the precise quantification of FLFA.