The junction temperature of LEDs is important for its life, reliability and efficacy. The existing transient measurement method of the junction temperature of using transient thermal tester (T3ster) based on the time-resolved measuring with a constant bias current according to the JESD51-14 is able to obtain the LED junction temperature rise based on the known temperature of thermostat module as the heatsink. In practice, without T3ster and the thermostat module, for multi-LED module with multiple heat sources in the luminaries, the thermal resistance matrix needs to be built to realize the thermal transfer between one another such that their junctions temperature raises can be calculated from their thermal power consumption. It is demonstrated that without measurement of the temperature heatsink temperature, the individual junction temperature of LEDs (groups) in multi-LED module with a thermistor (NTC or PTC) on its PCB measuring the local reference temperature can be obtained from the modified N x (N+1) thermal resistance matrix having N LED heat sources and N+1 junction temperature rise. A multi-LED module sample with 3 groups of LEDs has been studied at 5 different ambient temperatures and 2 additional different power combinations using 3 thermal resistance matrices built at 3 different ambient temperatures for comparison. The result showed that the modified method is effective and convenient for measurement of the junction temperature of the multi-LED modules with a similar accuracy comparing to the conventional one in the local reference temperature range of 20~100°C.