In order to optionally regulate embedding capacity and embedding transparency according to users requirements in voice-over-IP (VoIP) steganography, a dynamic matrix encoding strategy (DMES) was presented. Differing from the traditional matrix encoding strategy, DMES dynamically chose the size of each message group in a given set of adoptable message sizes. The appearance possibilities of all adoptable sizes were set in accordance with the desired embedding performance (embedding rate or bit-change rate). Accordingly, a searching algorithm that could provide an optimal combination of appearance possibilities was proposed. Furthermore, the roulette wheel algorithm was employed to determine the size of each message group according to the optimal combination of appearance possibilities. The effectiveness of DMES was evaluated in StegVoIP, which is a typical covert communication system based on VoIP. The experimental results demonstrate that DMES can adjust embedding capacity and embedding transparency effectively and flexibly, and achieve the desired embedding performance in any case. For the desired embedding rate, the average errors are not more than 0.000 8, and the standard deviations are not more than 0.002 0; for the desired bit-change rate, the average errors are not more than 0.001 4, and the standard deviations are not more than 0.002 6.