A novel microstructure fiber based on side-polished fiber (SPF) was demonstrated. Polystyrene microspheres were self-assembled onto the side-polished surface of SPF to form the colloidal crystal cladding of the microstructure fiber. Because of the Bragg reflection of the colloidal crystals cladding and the strong interaction between evanescent field and colloidal crystal, three main valleys were observed in the transmission spectrum. The modulation amplitude of the valley was up to 12 dB. Furthermore, the transmission valley showed a high sensitivity of temperature. At the wavelength of 1524.25 nm—the position of valley, transmission optical power showed a maximum optical power variation of 14.7 dB in the range of 20–50 °C, the sensitivity of temperature was up to 0.487 dB/°C. The linear correlation coefficient was 99.84%. This SPF with colloidal crystals cladding shows a good potential in fiber sensing and other photonic applications.