The rational allocation of heat and water provides favorable climatic conditions for agricultural production. It is important to make clear the matching and variation rule of heat and water for guiding agricultural production. Based on the data of daily precipitation and temperature from 1961 to 2014 in Northeast China agricultural zone (NCAZ), the variation law of inner-annual inhomogeneous distribution of precipitation (IIDP) and its response to regional warming in NCAZ were analyzed. The results show that: (1) In 1961-2014, the trends was found and characterized by decreasing IIDP, increasing inter-annual variation of IIDP and being more early precipitation concentration period (PCP) consistently in the whole NCAZ; (2) The decrease rate of IIDP was larger in the middle of NCAZ, contrast to smaller value in southern and northern part of NCAZ; (3) The IIDP depended on air temperature strongly, which showed obvious asynchronism and inter-regional difference with precipitation concentration degree (PCD) being behind air temperature on short period and beyond on long period mainly. In a more warming world, the advance of PCP keeps simultaneous heat and precipitation stable, but the decrease of IIDP and the increase of the inter-annual variation may increase the risk of summer drought in NCAZ. The results can provide a reference for formulating scientific farmland water management strategies.