The natural course of intermittent exotropia and the factors affecting its control has been unclear. We aim to report the natural course of our cohort of 117 Chinese children with intermittent exotropia and to identify baseline parameters that may have predictive value in the control deterioration of the disease. The visual acuity, spherical equivalent, compliance to orthoptic exercise, angle of deviation fusional convergence parameters and Newcastle Control Score were recorded for all children at baseline and at 3 years apart. Patients were divided into two groups according to the change in control over the 3 years: group 1 included patients who had no deterioration or had improvement in disease control; and group 2 were those who had deteriorated control or had undergone surgery. There were 77 patients (66%) in group 1 and 40 (34%) patients in group 2. Comparing the baseline parameters of the two groups, group 1 had statistically significantly smaller angle of deviation, larger fusional reserve, larger fusional recovery, and higher fusional reserve ratio (p < 0.05). Other baseline parameters were similar between the two groups. The baseline fusional parameters may have predictive value in determining the control of intermittent exotropia.