The harmonics of line to line voltage in two-stage matrix converter (TSMC) with fixed carrier frequency had discrete and high values and produced powerful electromagnetic interference (EMI). In this paper, chaotic carrier frequency modulation technique (CCFMT) was applied in TSMC for the first time to spread sideband range and suppress harmonic peak value. Although this technique could suppress EMI, it would increase the probability of narrow pulses. In order to improve reliability, the rectifier in the two-stage matrix converter uses PWM modulation with zero vector to extend the zero current commutation time, solves the narrow pulse problem, and simplifies the commutation process. At last, an experiment platform was designed and experimental results showed that harmonics of line to line voltage was efficiently suppressed.