For multiple-chip high power LED arrays, a high temperature uniformity among LED chips is the guarantee of optical performance, thermal stability and reliability of the devices. Single-layer microchannel heat sink (SMHS) is a good alternative to reach this goal, but its performance is limited because the water temperature may rise at the downstream of the channel. In this paper, a double-layer microchannel heat sink (DMHS) with counter water flow arrangement was proposed to decrease temperature difference among the LED chips. And a compact thermal model (CTM) was established to model thermal characteristics of the DMHS. By analogizing the thermal resistance to electrical resistance, the equations of the thermal networks were established following the Kirchhoff Current Law (KCL). The DMHS structure was optimized with the pump power fixed. Under the condition of inlet water temperature Tin=20°C, we obtained the case temperature of three chips, which were TC1=32.54°C, TC2=32.81°C and TC3=33.40°C respectively. The maximum temperature difference was 0.86°C among chips. Meanwhile, a CFD numerical simulation was conducted to examine the optimized structure. Simulation results showed that the temperature of three chips were TC1=32.14°C, TC2=32.39°C and TC3=32.52°C respectively, which matched well with the CTM. Compared to the SMHS under the same operating conditions, which achieved a temperature difference of 2.3°C, the DMHS significantly improve the temperature uniformity.