Carbon nanodots (C-dots) have gained much attention due to their unique optical and physicochemical properties. Herein, C-dots with uniform size have been fabricated via an in situ pyrolysis of dipropylamine (DPA) organic amines confined in the channels of SAPO-46 (AFS). The as-obtained C-dots@AFS composite material shows nonlinear optical property, which can be used as saturable absorber (SA) to generate Q-switched ytterbium-doped fiber laser (YDFL). By inserting the C-dots@AFS SA into an YDFL cavity pumped by a 980 nm laser diode, stable passively Q-switched fiber laser can be obtained for a threshold pump power of 220 mW, and 4.5 μs pulses with a repetition rate of 33.51 kHz can be obtained for a pump power of 380 mW. To the best of our knowledge, this is the first demonstration of a C-dots@AFS-based Q-switched fiber laser.