In order to meet the needs of on-site, accurate, fast, and remote detection, we design a smartphone-based handheld dual-channel optical fiber fluorescence sensor (DOFFS), which is composed of a semiconductor laser for exciting fluorescence signals, a smartphone with a dual-bandpass filter for collecting fluorescence signals, a fiber coupler for transmitting light, and batteries for laser power supply. All the components are integrated into a 3D printed shell, on the side of which there are two fiber flanges used for fiber probe connection. The fluorescence signals of green and red quantum dots modified on the fiber probes can be captured by the smartphone camera and calculated by a self-developed Android application. The comparisons of single-channel and dual-channel fluorescence signals with pH show that the performance of the sensor is good. The proposed sensor not only can simultaneously detect dual-channel signals for fast detection needs, but it also is handheld with a small size of 79×57×154mm3 and inner power supply, and the fiber probes can be easily replaced, supporting remote and on-site applications. It is a potential tool for many occasions in many fields.