Because of the unique advantages of mathematical model in experimental data integration and dynamical analysis of gene regulatory network, the application of mathematical model in the research of circadian rhythm has been paid more and more attention for the past few years. In mammals, circadian rhythms are controlled by the neurons located in the suprachiasmatic nucleus (SCN) of the hypothalamus. Each neuron in the SCN contains an autonomous molecular clock. The fundamental question is how the individual cellular oscillators, expressing a wide range of periods, interact and assemble to achieve phase synchronization. It is an effective way to study the phenomenon of life at the molecular level. With the help of mathematical methods of network analysis and cybernetics, biological networks can be constructed and then theoretical study and numerical simulation can be given by dint of knowledge of nonlinear dynamics. In this paper, the advances of mathematical modeling and dynamical analysis in mammalian circadian clocks are given from a systems biology view. At last, prospects for studying circadian rhythm are brought forward.