This work demonstrates a smartphone-based automated fluorescence analysis system (SAFAS) for point-of-care testing (POCT) of Hg(II). This system consists of three modules. The smartphone module is used to provide an excitation light source, and to collect and analyze fluorescent images. The dark box module is applied to integrate the desired optical elements and offers a dark environment. The cost of the integrated dark box mainly includes the upper cover, box body, lower bottom, fixture and some optical elements which is about $109. The chip module is used for fluorescence sensing, which is composed of an upper plate, bottom plate and cloth-based chip. Due to the integration of multiple smartphone functions, the SAFAS eliminates the need for additional power sources, light sources and analysis systems. The dark box and upper and bottom plates are made by 3D printer. The cloth-based chip (about $0.005 for each chip) is fabricated using the wax screen-printing technique, with no need for expensive and complex fabrication equipments. To our knowledge, the cloth-based microfluidic fluorescence detection method combined with smartphone functions is first reported. By using optimal conditions, the designed system can realize the quantitative detection of Hg(II), which has a linear range of 0.001–100$$$\mu$g$$mL${}^{?1}$ and a detection limit of 0.5$$ng$$mL${}^{?1}$. Additionally, the SAFAS has been successfully applied for detecting Hg(II) in actual water samples, with recoveries of 100.1%–111%, RSDs of 3.88%–9.74%, and fast detection time of about 1 min. Obviously, the proposed SAFAS has the advantages of high sensitivity, wide dynamic range, acceptable reproducibility, good stability and low cost. Therefore, it is believed that the presented SAFAS has great potential to perform the POCT of Hg(II) in different water samples.This work demonstrates a smartphone-based automated fluorescence analysis system (SAFAS) for point-of-care testing (POCT) of Hg(II). This system consists of three modules. The smartphone module is used to provide an excitation light source, and to collect and analyze fluorescent images. The dark box module is applied to integrate the desired optical elements and offers a dark environment. The cost of the integrated dark box mainly includes the upper cover, box body, lower bottom, fixture and some optical elements which is about $109. The chip module is used for fluorescence sensing, which is composed of an upper plate, bottom plate and cloth-based chip. Due to the integration of multiple smartphone functions, the SAFAS eliminates the need for additional power sources, light sources and analysis systems. The dark box and upper and bottom plates are made by 3D printer. The cloth-based chip (about $0.005 for each chip) is fabricated using the wax screen-printing technique, with no need for expensive and complex fabrication equipments. To our knowledge, the cloth-based microfluidic fluorescence detection method combined with smartphone functions is first reported. By using optimal conditions, the designed system can realize the quantitative detection of Hg(II), which has a linear range of 0.001–100$$$\mu$g$$mL${}^{?1}$ and a detection limit of 0.5$$ng$$mL${}^{?1}$. Additionally, the SAFAS has been successfully applied for detecting Hg(II) in actual water samples, with recoveries of 100.1%–111%, RSDs of 3.88%–9.74%, and fast detection time of about 1 min. Obviously, the proposed SAFAS has the advantages of high sensitivity, wide dynamic range, acceptable reproducibility, good stability and low cost. Therefore, it is believed that the presented SAFAS has great potential to perform the POCT of Hg(II) in different water samples.