Using FY2D TBB data, radar echo data, routine meteorological data, precipitation data of automatic weather stations, NCEP 1°×1° reanalysis data etc. are analyzed characteristics of mesoscale convective system (MCS) and its effects on short time extremely heavy precipitation in Sichuan Basin during 21-22 July 2012. The results show that: (1) This precipitation process has two significant 6 h short time severe rainfall stages. The first stage is from 00:00 to 06:00 BT 21 July 2012, and the second is from 21:00 BT 21 to 03:00 BT 22 July 2012. In the first stage, the short time severe rainfall in western Sichuan Basin is caused by MCS, which is affected by 500 hPa plateau vortex and 700 hPa low vortex shear line. In the second stage, the extremely heavy rain is caused by the 500 hPa plateau vortex and 700 hPa southwest low vortex. (2) Short time severe rainfalls are usually caused by deep convections in MCS. In its developing process, MCS is in meso βscale or meso γ scale, having the features of low TBB values, big radar reflectivity factors and high VIL values. (3) The analysis of sounding data shows that unstable energy of atmosphere is high, CAPE value is large and vertical wind shear is dramatic during the early stage of MCS. The interaction areas of low level cold and warm temperature advections are beneficial to induce MCS, and the temperature gradient is high in these areas. Also during different developing periods, the structure of MCS shows positive vorticity and negative divergence in low level, while negative vorticity and positive divergence exist in high level. Such physical structure is an important factor for MCS to develop and maintain, and it is also one physical mechanism for short time severe precipitation.