Попробуйте этот код:
import matplotlib.pyplot as plt
from matplotlib import dates
# fake data
arr_data = range(0, 4)
arr_secs = [52000, 53000, 54000, 55000]
# format seconds to date with this format '%H:%M:%S'
arr__secs_formatted = list(map(datetime.datetime.strptime, map(lambda s: time.strftime('%H:%M:%S', time.gmtime(s)), arr_secs), len(arr_secs)*['%H:%M:%S']))
fig, ax = plt.subplots()
ax.plot(arr_data, arr_secs_formatted, 'ro-')
# set your date formatter whit this format '%H:%M'
formatter = dates.DateFormatter('%H:%M')
ax.yaxis.set_major_formatter(formatter)
plt.show()
![enter image description here](https://i.stack.imgur.com/KRg4x.png)