Liquid control in microchannels is quite important in microfluidic devices used in, for example, lab-on-a-chip and point-of-care applications. Capillary microfluidics, being self-powered, is especially advantageous for use in passive devices, and has attracted significant attention. In this paper, capillary flows in rectangular microchannels with spacers are studied experimentally and theoretically; in particular, capillary flow synchronization (or waiting) behavior is identified and investigated. Based on changes of channel walls, two basic synchronization modes are proposed for flows isolated by spacers in a channel. Experimental results show that the velocities of faster capillary flows are reduced by the liquid pinning effect and that the time delay between two capillary flows is automatically balanced. The synchronization behavior of capillary flows is explained by analyzing the time delay, contact angle variation, and capillary forces. In addition, the quantity of liquid flowing out of the waiting channels is estimated and verified. Then a model for the change in contact angle during synchronization is derived and verified. Finally, we conceive a series of studies of the control of capillary flows for different spacer designs and conduct an experiment to study the dynamic behaviors of a number of capillary flows by adding many spacers in a microchannel. This study expands the applications of capillary microfluidics.