Interleaver has been one of the key components in the wave division multiple (WDM) communication system. Cascaded Mach-Zehnder (M-Z) polymer interleaver by planar lightwave circuit (PLC) technique has great advantages of high performance and mass production. The performance optimization and tolerance calculation are critical in practical designs. This paper presents the design method and results of such high performance polymer waveguide interleaver with large tolerance.First, four targets parameters are given to judge a interleaver's optical performance. Second, use the Jones Matrix the key parameters, couple ratios of 3 couplers, are calculated to meet the high performance. The optimal values are acquired by compromise with 3-D tolerance design to ensure as large as possible couple ratio tolerance. Then with such ratio tolerance the waveguide structure is optimized to achieve the large index tolerance of waveguide material by effective index method with build-in perturbation correction (EIMPC). Finally in our design the high performance can be guaranteed within the large index variations of BCB material.