We propose photonic crystal substrates that support microstrip structures to mitigate the problem of spurious harmonics in microwave devices. The wave propagation in microwave transmission lines can be controlled by employing substrates that have modulated dielectric constant such that there exist forbidden spectral regions, which are known as bandgaps in the photonic crystal terminology. With proper selection of crystalline geometry, these bandgaps can be designed to suppress the spurious harmonics. To show the existence of bandgaps in microstrip structures, we present Bloch analysis with a bi-layered photonic crystal configuration of high and low permittivities. For a practical microstrip structure that incorporates a bi-layered photonic crystal substrate, we show suppression of spurious harmonics via circuit analysis and transmittance measurements. Furthermore, a 2.5 GHz coupled-line filter is designed on a photonic crystal substrate, and 30 dB second harmonic suppression at 5 GHz is experimentally demonstrated. With the current trend multiple device integration on single platform, the photonic crystal substrates can potentially provide the noise suppression and spurious harmonic rejection needed for microwave components occupying close proximity.