From July to August in 2012, we recorded and analyzed the relationship between call structure and body size, snout-vent length, and head width in 55 male Phrynoglossus martensii. The results show that body size, snout-vent length, and head width were 1.26 ± 0.55 g, 21.04 ± 2.57 mm, and 6.76 ± 0.75 mm, respectively. This frog produces only the advertisement call and aggressive call. The advertisement call consists of a single note, with dominant and fundamental frequencies at 1519.69 ± 70.60 Hz, range 1057 ~ 1765Hz and 1519.69 ± 70.60 Hz, range 1057–1765Hz, respectively. Remarkably, both the dominant and fundamental frequencies of the advertisement call were negatively correlated with body size and snout-vent length, whereas the inter-note intervals were positively correlated with body size and head. The dominant and fundamental frequencies of the aggressive call were 3752.64 ± 174.47 Hz, range 3304 ~ 4081 Hz and 1674.88 ± 79.88 Hz, range 1367–1870 Hz, respectively. Compared with the advertisement call, the fundamental frequencies (t = – 5.374, df = 56, P < 0.001) were much higher and the note duration and inter-note intervals were much lower in the aggressive call (P < 0.05). These results demonstrate that individual variations in call structure and types are mainly dependent on morphological indexes in this species with small body mass.